annotate iReport.xml @ 9:7300ed4c1481 draft default tip

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author saskia-hiltemann
date Mon, 04 Sep 2017 10:49:00 -0400
parents 86219e4aa239
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1 <tool id="iReport" name="iReport" version="1.1">
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2
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3 <!-- Note to Galaxy Admins:
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4 This wrapper contains one hidden parameter with hardcoded server location, this is currently needed for dalliance genome browser to function correctly,
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5 please change this value as needed! (see below for parameter: <param name="localhost" type="hidden" value="https://bioninf-galaxian.erasmusmc.nl"/>)
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6 -->
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7 <description> create an HTML report </description>
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8
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9 <command><![CDATA[
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10
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11 #set $labelb64 = str($label).encode('base64').replace('\n','')
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12 #set $coverimageb64 = str($coverimage).encode('base64').replace('\n','')
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13
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14 '$__tool_directory__'/iReport.sh
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15 --toolpath '$__tool_directory__'
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16 --galaxypath ${report.files_path}
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17 --htmlout ${report}
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18 --minwidth ${minwidth}
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19 --coverimage -${coverimageb64}
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20 #for $i, $t in enumerate($tabs)
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21 #set $tabtitleb64 = str($t.tabtitle).encode('base64').replace('\n','')
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22 --tab ${tabtitleb64}
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23 #for $j, $u in enumerate($t.content)
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24 #if $u.filetype.itemtype == "image"
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25 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.zoomlevel}:${u.filetype.zoomenable}:${u.filetype.align}"
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26 #else if $u.filetype.itemtype == "table"
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27 #if $u.filetype.collink.columnhyperlink == "Y"
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28 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.fancy}:Y:${u.filetype.collink.urlcol}:${u.filetype.collink.urlprefix}:${u.filetype.collink.urlsuffix}:${u.filetype.collink.urlitems}:${u.filetype.minw}:${u.filetype.minh}"
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29 #else
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30 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.fancy}:N:${u.filetype.minw}:${u.filetype.minh}"
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31 #end if
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32 #else if $u.filetype.itemtype == "link"
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33 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${__app__.security.encode_id($u.filetype.item.id)}:${u.filetype.ireport}:${u.filetype.item2}:${localhost}:${proxy}"
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34 #else if $u.filetype.itemtype == "weblink"
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35 #set $itemb64 = str($u.filetype.item).encode('base64').replace('\n','')
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36 #set $item2b64 = str($u.filetype.item2).encode('base64').replace('\n','')
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37 --item "${t.tabtitle}:${u.filetype.itemtype}:${itemb64}:${u.filetype.break}:${item2b64}"
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38 #else if $u.filetype.itemtype == "text"
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39 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"
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40 #else if $u.filetype.itemtype == "textfile"
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41 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"
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42 #else if $u.filetype.itemtype == "htmlfile"
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43 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}:${__app__.security.encode_id($u.filetype.item.id)}:${u.filetype.ireport}:${localhost}:${proxy}"
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44 #else if $u.filetype.itemtype == "htmlpage"
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45 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}"
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46 #else if $u.filetype.itemtype == "genomebrowser"
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47 #set $itemb64 = str($u.filetype.initialview).encode('base64').replace('\n','')
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48 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.genomebuild}:${u.filetype.break}:${__app__.security.encode_id($report.id)}:${localhost}:${itemb64}"
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49 --newgb "-"
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50 #for $k, $gb in enumerate($u.filetype.gbtracks)
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51 --genomebrowsertrack ${gb.item}:${gb.tracklabel}:${gb.gbfiletype}
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52 #end for
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53 #else
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54 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}"
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55 #end if
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56 #end for
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57 #end for
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58 --label ${labelb64}
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59
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60 ]]></command>
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61 <inputs>
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62 <!-- this sucks, but need to hardcode where galaxy is running from for some components -->
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63 <param name="localhost" type="hidden" value="https://bioinf-galaxian.erasmusmc.nl/galaxy">
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64 <sanitizer>
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65 <valid initial="default">
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66 <add preset="string.printable"/>
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67 <remove value=":"/>
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68 </valid>
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69 <mapping initial="none">
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70 <add source=":" target="==colon=="/>
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71 </mapping>
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72 </sanitizer>
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73 </param>
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74 <param name="proxy" type="hidden" value="galaxy"/>
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75 <!-- /sucks -->
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76
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77
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78 <param name="label" type="text" size="100" label="Name of Report" >
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79 <sanitizer>
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80 <valid initial="default">
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81 <add preset="string.printable"/>
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82 <remove value=":"/>
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83 <remove value="$"/>
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84 <remove value="~"/>
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85 <remove value="("/>
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86 <remove value=")"/>
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87 <remove value="&lt;"/>
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88 <remove value="&gt;"/>
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89 </valid>
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90 <mapping initial="none">
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91 <add source="&lt;" target="&amp;#60;"/>
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92 <add source="&gt;" target="&amp;#62;"/>
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93 <add source=":" target="&amp;#58;"/>
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94 <add source="$" target="&amp;#36;"/>
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95 <add source="~" target="&amp;#126;"/>
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96 <add source=")" target="&amp;#41;"/>
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97 <add source="(" target="&amp;#40;"/>
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98
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99 </mapping>
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100 </sanitizer>
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101 <validator type="empty_field" />
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102 </param>
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103 <param name="coverimage" type="text" size="100" label="Link to cover image" help="Optional. A default image will be used if not specified">
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104 <sanitizer>
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105 <valid initial="default">
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106 <add preset="string.printable"/>
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107 <remove value=" "/>
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108 <remove value=":"/>
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109 <remove value="$"/>
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110 <remove value="~"/>
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111 <remove value="("/>
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112 <remove value=")"/>
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113 <remove value="&lt;"/>
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114 <remove value="&gt;"/>
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115 </valid>
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116 <mapping initial="none">
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117 <add source=" " target=""/>
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118 <add source="&lt;" target="&amp;#60;"/>
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119 <add source="&gt;" target="&amp;#62;"/>
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120 <add source=":" target="&amp;#58;"/>
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121 <add source="$" target="&amp;#36;"/>
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122 <add source="~" target="&amp;#126;"/>
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123 <add source=")" target="&amp;#41;"/>
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124 <add source="(" target="&amp;#40;"/>
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125 </mapping>
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126 </sanitizer>
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127 </param>
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128
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129 <param name="minwidth" type="integer" min="0" max="5000" value="1200" label="Width of page (in pixels)" />
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130 <repeat name="tabs" title="Tab" default="1" >
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131 <param name="tabtitle" type="text" size="50" label="Enter tab name">
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132 <sanitizer>
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133 <valid initial="default">
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134 <add preset="string.printable"/>
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135 <remove value=":"/>
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136 <remove value=" "/>
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137 <remove value="$"/>
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138 <remove value="~"/>
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139 <remove value="&lt;"/>
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140 <remove value="&gt;"/>
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141 <remove value="("/>
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142 <remove value=")"/>
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143 </valid>
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144 <mapping initial="none">
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145 <add source=":" target="&amp;#58;"/>
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146 <add source=" " target="&amp;#32;"/>
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147 <add source="$" target="&amp;#36;"/>
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148 <add source="~" target="&amp;#126;"/>
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149 <add source=")" target="&amp;#41;"/>
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150 <add source="(" target="&amp;#40;"/>
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151 </mapping>
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152 </sanitizer>
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153 <validator type="empty_field" />
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154 </param>
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155 <repeat name="content" title="Content-Item" default="1">
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156 <conditional name="filetype">
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157 <param name="itemtype" type="select" label="Select Item Type" >
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158 <option value="" > Please choose item type </option>
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159 <option value="text" > Text Field </option>
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160 <option value="textfile" > Text File from history </option>
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161 <option value="htmlfile"> HTML File from history </option>
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162 <option value="htmlpage"> iFrame with HTML page from web </option>
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163 <option value="image"> Image </option>
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164 <option value="pdf" > PDF File </option>
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165 <option value="table"> Table </option>
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166 <option value="link" > Link to Dataset </option>
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167 <option value="links"> Links to Files in Archive Dataset </option>
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parents: 6
diff changeset
168 <option value="weblink" > Web link </option>
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saskia-hiltemann
parents: 6
diff changeset
169 <option value="genomebrowser" > Genome Browser (beta) </option>
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parents: 6
diff changeset
170 <validator type="empty_field" />
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saskia-hiltemann
parents: 6
diff changeset
171 </param>
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parents: 6
diff changeset
172
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parents: 6
diff changeset
173 <!--###########################
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parents: 6
diff changeset
174 # Text Field #
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parents: 6
diff changeset
175 ########################### -->
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saskia-hiltemann
parents: 6
diff changeset
176 <when value="text">
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parents: 6
diff changeset
177 <param name="md" type="boolean" truevalue="Y" falsevalue="n" checked="false" label="Text in MarkDown format?" help="If checked, text file or field will be interpreted as markdown"/>
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diff changeset
178 <param name="item" type="text" area="true" size="10x100" label="Text to display." help="can explicitly add whitespace adding \n in your text for a newline or \t for a tab. HTML tags em, strong, b, i, h1-h6 tags" >
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parents: 6
diff changeset
179 <sanitizer>
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parents: 6
diff changeset
180 <valid initial="default">
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parents: 6
diff changeset
181 <add preset="string.printable"/>
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saskia-hiltemann
parents: 6
diff changeset
182 <remove value="\"/>
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saskia-hiltemann
parents: 6
diff changeset
183 <remove value="/"/>
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saskia-hiltemann
parents: 6
diff changeset
184 <remove value=","/>
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saskia-hiltemann
parents: 6
diff changeset
185 <remove value=":"/>
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saskia-hiltemann
parents: 6
diff changeset
186 <remove value="~"/>
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saskia-hiltemann
parents: 6
diff changeset
187 <remove value="&lt;"/>
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saskia-hiltemann
parents: 6
diff changeset
188 <remove value="&gt;"/>
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saskia-hiltemann
parents: 6
diff changeset
189 <remove value="&apos;"/>
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saskia-hiltemann
parents: 6
diff changeset
190 <remove value="&quot;"/>
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saskia-hiltemann
parents: 6
diff changeset
191 <remove value="&#xA;"/>
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saskia-hiltemann
parents: 6
diff changeset
192 <remove value="&#xD;"/>
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saskia-hiltemann
parents: 6
diff changeset
193 <remove value="&amp;"/>
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saskia-hiltemann
parents: 6
diff changeset
194 <remove value="&#x3a;"/>
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saskia-hiltemann
parents: 6
diff changeset
195 <remove value=" "/>
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saskia-hiltemann
parents: 6
diff changeset
196 <remove value="`"/>
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saskia-hiltemann
parents: 6
diff changeset
197 <remove value="$"/>
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saskia-hiltemann
parents: 6
diff changeset
198 <remove value="|"/>
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saskia-hiltemann
parents: 6
diff changeset
199 </valid>
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saskia-hiltemann
parents: 6
diff changeset
200 <mapping initial="none">
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saskia-hiltemann
parents: 6
diff changeset
201 <add source="\" target="\\"/>
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saskia-hiltemann
parents: 6
diff changeset
202 <add source="/" target="==slash=="/>
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saskia-hiltemann
parents: 6
diff changeset
203 <add source="&amp;" target="&amp;&amp;"/>
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saskia-hiltemann
parents: 6
diff changeset
204 <add source="&#xA;" target="&amp;n"/>
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saskia-hiltemann
parents: 6
diff changeset
205 <add source="&#xD;" target="&amp;r"/>
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saskia-hiltemann
parents: 6
diff changeset
206 <add source="&#x3a;" target="&amp;c"/>
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saskia-hiltemann
parents: 6
diff changeset
207 <add source=" " target="==space=="/>
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saskia-hiltemann
parents: 6
diff changeset
208 <add source="," target="==comma=="/>
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saskia-hiltemann
parents: 6
diff changeset
209 <add source="&lt;" target="==lt=="/>
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saskia-hiltemann
parents: 6
diff changeset
210 <add source="&gt;" target="==gt=="/>
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saskia-hiltemann
parents: 6
diff changeset
211 <add source="&apos;" target="==apos=="/>
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saskia-hiltemann
parents: 6
diff changeset
212 <add source="&quot;" target="==quote=="/>
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saskia-hiltemann
parents: 6
diff changeset
213 <add source=":" target="&amp;#58;"/>
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saskia-hiltemann
parents: 6
diff changeset
214 <add source="`" target="==backtick=="/>
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saskia-hiltemann
parents: 6
diff changeset
215 <add source="$" target="==dollar=="/>
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saskia-hiltemann
parents: 6
diff changeset
216 <add source="|" target="==bar=="/>
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saskia-hiltemann
parents: 6
diff changeset
217 <add source="~" target="&amp;#126;"/>
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saskia-hiltemann
parents: 6
diff changeset
218 </mapping>
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saskia-hiltemann
parents: 6
diff changeset
219 </sanitizer>
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parents: 6
diff changeset
220 <validator type="empty_field" />
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parents: 6
diff changeset
221 </param>
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parents: 6
diff changeset
222 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?"/>
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parents: 6
diff changeset
223 </when>
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parents: 6
diff changeset
224
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parents: 6
diff changeset
225 <!--###########################
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saskia-hiltemann
parents: 6
diff changeset
226 # Text File #
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saskia-hiltemann
parents: 6
diff changeset
227 ########################### -->
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saskia-hiltemann
parents: 6
diff changeset
228 <when value="textfile">
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diff changeset
229 <param name="md" type="boolean" truevalue="Y" falsevalue="n" checked="false" label="Text in MarkDown format?" help="If checked, text file or field will be interpreted as markdown. Will use pandoc if this is installed on the system, else uses a custom script"/>
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parents: 6
diff changeset
230 <param name="item" type="data" label="Text File" help="Text file to display verbatim"/>
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parents: 6
diff changeset
231 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout"/>
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parents: 6
diff changeset
232 </when>
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parents: 6
diff changeset
233
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parents: 6
diff changeset
234 <!--###########################
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saskia-hiltemann
parents: 6
diff changeset
235 # HTML File #
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saskia-hiltemann
parents: 6
diff changeset
236 ########################### -->
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saskia-hiltemann
parents: 6
diff changeset
237 <when value="htmlfile">
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saskia-hiltemann
parents: 6
diff changeset
238 <param name="item" type="data" label="HTML File" help="Contents of html file will be displayed in an iframe"/>
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saskia-hiltemann
parents: 6
diff changeset
239 <param name="ireport" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is the link another iReport?"/>
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parents: 6
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240 <param name="height" type="integer" min="0" max="500000" value="350" label="Height (in pixels)" help="Height of the iFrame displaying the html page"/>
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parents: 6
diff changeset
241 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout"/>
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parents: 6
diff changeset
242 </when>
6
42076db43d42 Fixed auto resizing plus various other minor bugs
saskia-hiltemann
parents: 5
diff changeset
243
7
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parents: 6
diff changeset
244 <when value="htmlpage">
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parents: 6
diff changeset
245 <param name="item" type="text" label="URL" size="100" help="Contents of webpage will be displayed in an iframe">
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parents: 6
diff changeset
246 <sanitizer>
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saskia-hiltemann
parents: 6
diff changeset
247 <valid initial="default">
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saskia-hiltemann
parents: 6
diff changeset
248 <add preset="string.printable"/>
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saskia-hiltemann
parents: 6
diff changeset
249 <remove value="&amp;"/>
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saskia-hiltemann
parents: 6
diff changeset
250 <remove value=":"/>
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saskia-hiltemann
parents: 6
diff changeset
251 <remove value="/"/>
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saskia-hiltemann
parents: 6
diff changeset
252 <remove value=" "/>
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saskia-hiltemann
parents: 6
diff changeset
253 <remove value="$"/>
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saskia-hiltemann
parents: 6
diff changeset
254 <remove value="~"/>
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saskia-hiltemann
parents: 6
diff changeset
255 <remove value="("/>
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saskia-hiltemann
parents: 6
diff changeset
256 <remove value=")"/>
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saskia-hiltemann
parents: 6
diff changeset
257 </valid>
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saskia-hiltemann
parents: 6
diff changeset
258 <mapping initial="none">
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saskia-hiltemann
parents: 6
diff changeset
259 <add source="&amp;" target="&amp;#38;"/>
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saskia-hiltemann
parents: 6
diff changeset
260 <add source=":" target="&amp;#58;"/>
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saskia-hiltemann
parents: 6
diff changeset
261 <add source="/" target="&amp;#47;"/>
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saskia-hiltemann
parents: 6
diff changeset
262 <add source=" " target="&amp;#32;"/>
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saskia-hiltemann
parents: 6
diff changeset
263 <add source="$" target="&amp;#36;"/>
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saskia-hiltemann
parents: 6
diff changeset
264 <add source="~" target="&amp;#126;"/>
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saskia-hiltemann
parents: 6
diff changeset
265 <add source="~" target="&amp;#126;"/>
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saskia-hiltemann
parents: 6
diff changeset
266 <add source=")" target="&amp;#41;"/>
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saskia-hiltemann
parents: 6
diff changeset
267 <add source="(" target="&amp;#40;"/>
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saskia-hiltemann
parents: 6
diff changeset
268 </mapping>
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saskia-hiltemann
parents: 6
diff changeset
269 </sanitizer>
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diff changeset
270 </param>
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saskia-hiltemann
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diff changeset
271 <param name="height" type="integer" min="0" max="500000" value="350" label="Height (in pixels)" help="Height of the iFrame displaying the html page"/>
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272 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout"/>
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saskia-hiltemann
parents: 6
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273 </when>
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saskia-hiltemann
parents: 6
diff changeset
274
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saskia-hiltemann
parents: 6
diff changeset
275 <!--###########################
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saskia-hiltemann
parents: 6
diff changeset
276 # Images #
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saskia-hiltemann
parents: 6
diff changeset
277 ########################### -->
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saskia-hiltemann
parents: 6
diff changeset
278 <when value="image">
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saskia-hiltemann
parents: 6
diff changeset
279 <param name="item" type="data" label="Image File" format="png,svg,jpg,jpeg" help="Supported formats: png, jpg, svg. If image is scaled by choice of width, zoom-on-mousover effect is added."/>
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parents: 6
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280 <param name="zoomlevel" type="integer" min="0" max="5000" value="250" label="Width (in pixels)" help="enter 0 to keep original size" />
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parents: 6
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281 <param name="zoomenable" type="boolean" checked="True" truevalue="Y" falsevalue="N" label="Enable zoom-on-mouseover effect?" help="If checked and nonzero width, zoom-on-mousover effect added"/>
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parents: 6
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282 <param name="align" type="select" label="Alignment of image (float)" help="Use left or right align to have images and text next to each other. Always specify image first (with alignment), then text, if you want to show them side by side." >
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parents: 6
diff changeset
283 <option value="none" > default (recommended) </option>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
284 <option value="left" > left </option>
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saskia-hiltemann
parents: 6
diff changeset
285 <option value="right" > right </option>
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saskia-hiltemann
parents: 6
diff changeset
286 <option value="middle"> center </option>
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saskia-hiltemann
parents: 6
diff changeset
287 <!--<option value="top"> top </option>
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saskia-hiltemann
parents: 6
diff changeset
288 <option value="bottom"> bottom </option>-->
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saskia-hiltemann
parents: 6
diff changeset
289 </param>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
290 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout"/>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
291 </when>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
292
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
293 <!--###########################
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
294 # Table #
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saskia-hiltemann
parents: 6
diff changeset
295 ########################### -->
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
296 <when value="table">
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saskia-hiltemann
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297 <param name="item" type="data" label="Table File" help="must be a tab-delimited file with a 1-line header" />
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parents: 6
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298 <param name="fancy" type="boolean" checked="True" truevalue="Y" falsevalue="N" label="Fancy table)?" help="If selected, will create, sortable, searchable, paginated table. Otherwise not (for small tables)"/>
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parents: 6
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299 <param name="minw" type="integer" value="0" label="Minimum width of table (in pixels)" help="only needed when tables are not displaying correctly"/>
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saskia-hiltemann
parents: 6
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300 <param name="minh" type="integer" value="0" label="Minimum height of table (in pixels)" help="only needed when tables are not displaying correctly"/>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
301 <conditional name="collink">
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parents: 6
diff changeset
302 <param name="columnhyperlink" type="select" label="create url links from one of the columns in your table?" help="For example: from column with gene names, link to genecards page">
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parents: 6
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303 <option value="N"> No </option>
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saskia-hiltemann
parents: 6
diff changeset
304 <option value="Y"> Yes </option>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
305 </param>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
306 <when value="Y">
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saskia-hiltemann
parents: 6
diff changeset
307 <param name="urlcol" type="data_column" data_ref="item" multiple="False" label="Column to turn in to weblinks" />
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saskia-hiltemann
parents: 6
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308 <param name="urlprefix" type="text" size="75" label="URL prefix" help="this will be placed before value in column to form the weblink. e.g. for genecards use: http://www.genecards.org/cgi-bin/carddisp.pl?gene=">
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saskia-hiltemann
parents: 6
diff changeset
309 <sanitizer>
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saskia-hiltemann
parents: 6
diff changeset
310 <valid initial="default">
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saskia-hiltemann
parents: 6
diff changeset
311 <add preset="string.printable"/>
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saskia-hiltemann
parents: 6
diff changeset
312 <remove value="&amp;"/>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
313 <remove value=":"/>
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saskia-hiltemann
parents: 6
diff changeset
314 <remove value="/"/>
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saskia-hiltemann
parents: 6
diff changeset
315 <remove value=" "/>
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saskia-hiltemann
parents: 6
diff changeset
316 <remove value="~"/>
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saskia-hiltemann
parents: 6
diff changeset
317 <remove value="("/>
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saskia-hiltemann
parents: 6
diff changeset
318 <remove value=")"/>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
319 </valid>
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saskia-hiltemann
parents: 6
diff changeset
320 <mapping initial="none">
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saskia-hiltemann
parents: 6
diff changeset
321 <add source="&amp;" target="==amp=="/>
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saskia-hiltemann
parents: 6
diff changeset
322 <add source=":" target="==colon=="/>
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saskia-hiltemann
parents: 6
diff changeset
323 <add source="/" target="//"/>
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saskia-hiltemann
parents: 6
diff changeset
324 <add source=" " target=""/>
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saskia-hiltemann
parents: 6
diff changeset
325 <add source="~" target="&amp;#126;"/>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
326 <add source=")" target="&amp;#41;"/>
0f2b740536fb Uploaded
saskia-hiltemann
parents: 6
diff changeset
327 <add source="(" target="&amp;#40;"/>
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saskia-hiltemann
parents: 6
diff changeset
328 </mapping>
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saskia-hiltemann
parents: 6
diff changeset
329 </sanitizer>
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saskia-hiltemann
parents: 6
diff changeset
330 </param>
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saskia-hiltemann
parents: 6
diff changeset
331 <param name="urlsuffix" type="text" size="75" label="URL suffix" help="this will be placed before value in column to form the weblink. e.g. For genecards, there is no suffix">
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saskia-hiltemann
parents: 6
diff changeset
332 <sanitizer>
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saskia-hiltemann
parents: 6
diff changeset
333 <valid initial="default">
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saskia-hiltemann
parents: 6
diff changeset
334 <add preset="string.printable"/>
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saskia-hiltemann
parents: 6
diff changeset
335 <remove value="&amp;"/>
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parents: 6
diff changeset
336 <remove value="/"/>
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parents: 6
diff changeset
337 <remove value=" "/>
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saskia-hiltemann
parents: 6
diff changeset
338 <remove value="~"/>
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saskia-hiltemann
parents: 6
diff changeset
339 <remove value="("/>
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saskia-hiltemann
parents: 6
diff changeset
340 <remove value=")"/>
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parents: 6
diff changeset
341 </valid>
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parents: 6
diff changeset
342 <mapping initial="none">
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parents: 6
diff changeset
343 <add source="&amp;" target="&amp;&amp;"/>
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parents: 6
diff changeset
344 <add source="/" target="//"/>
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parents: 6
diff changeset
345 <add source=" " target=""/>
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parents: 6
diff changeset
346 <add source="~" target="&amp;#126;"/>
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parents: 6
diff changeset
347 <add source=")" target="&amp;#41;"/>
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parents: 6
diff changeset
348 <add source="(" target="&amp;#40;"/>
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parents: 6
diff changeset
349 </mapping>
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parents: 6
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350 </sanitizer>
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diff changeset
351 </param>
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352 <param name="urlitems" type="data" label="(Not yet implemented) Archive with files to link to" optional="true" help="Optional. Only if you want to link column entries to local files instead of websites" format="data,tar.gz,zip,gz,bz2,tar"/>
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353 </when>
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354 </conditional>
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355 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout"/>
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356 </when>
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parents: 6
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357
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parents: 6
diff changeset
358 <!--###########################
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359 # PDF File #
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parents: 6
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360 ########################### -->
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361 <when value="pdf">
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362 <param name="item" type="data" label="PDF File" format="pdf"/>
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363 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout"/>
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364 </when>
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parents: 6
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365
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parents: 6
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366 <!--###########################
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367 # Links #
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368 ########################### -->
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369 <when value="link">
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370 <param name="item" type="data" label="File to link to" />
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371 <param name="item2" type="text" size="100" label="link text" help="text to display as a link"/>
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372 <param name="ireport" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is the link another iReport?"/>
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373 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout"/>
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374 </when>
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375
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376 <when value="links">
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377 <param name="item" type="data" label="Archive with files to link to" help="links will be created to each file in the archive. Supported formats: zip, gz, tar, bz2"/>
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378 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout" />
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379 </when>
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380
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381 <when value="weblink">
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382 <param name="item" type="text" size="100" label="web location to link to " help="url to link to">
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383 <sanitizer>
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384 <valid initial="default">
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385 <add preset="string.printable"/>
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parents: 6
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386 <remove value=" "/>
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parents: 6
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387 <remove value="&lt;"/>
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388 <remove value="&gt;"/>
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parents: 6
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389 <remove value="~"/>
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parents: 6
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390 <remove value="("/>
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parents: 6
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391 <remove value=")"/>
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392 </valid>
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parents: 6
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393 <mapping initial="none">
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parents: 6
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394 <add source=" " target=""/>
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parents: 6
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395 <add source="&lt;" target="&amp;#60;"/>
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parents: 6
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396 <add source="&gt;" target="&amp;#62;"/>
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parents: 6
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397 <add source=" " target="&amp;#32;"/>
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parents: 6
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398 <add source=")" target="&amp;#41;"/>
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parents: 6
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399 <add source="(" target="&amp;#40;"/>
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parents: 6
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400 </mapping>
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401 </sanitizer>
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402 </param>
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403 <param name="item2" type="text" size="100" label="link text" help="text to display as a link. If left empty, url itself will be the link text">
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404 <sanitizer>
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405 <valid initial="default">
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saskia-hiltemann
parents: 6
diff changeset
406 <add preset="string.printable"/>
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saskia-hiltemann
parents: 6
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407 <remove value="&lt;"/>
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saskia-hiltemann
parents: 6
diff changeset
408 <remove value="&gt;"/>
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saskia-hiltemann
parents: 6
diff changeset
409 <remove value="~"/>
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saskia-hiltemann
parents: 6
diff changeset
410 <remove value=" "/>
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saskia-hiltemann
parents: 6
diff changeset
411 <remove value="("/>
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parents: 6
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412 <remove value=")"/>
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parents: 6
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413 </valid>
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parents: 6
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414 <mapping initial="none">
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parents: 6
diff changeset
415 <add source="&lt;" target="&amp;#60;"/>
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parents: 6
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416 <add source="&gt;" target="&amp;#62;"/>
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parents: 6
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417 <add source="~" target="&amp;#126;"/>
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parents: 6
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418 <add source=" " target="&amp;#32;"/>
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parents: 6
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419 <add source=")" target="&amp;#41;"/>
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parents: 6
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420 <add source="(" target="&amp;#40;"/>
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parents: 6
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421 </mapping>
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parents: 6
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422 </sanitizer>
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423 </param>
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424 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout"/>
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425 </when>
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426
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diff changeset
427 <!--###########################
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428 # Genome Browser #
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429 ########################### -->
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430 <when value="genomebrowser">
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431 <!-- TODO: hardcoded server location needed for dalliance to function correctly! Change as needed! -->
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432
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433 <param name="genomebuild" type="select" label="Select Genome build to be used for Genome Browser" help="A Bio-Dalliance genome browser will be embedded into your iReport ">
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434 <option value="hg18" > hg18 </option>
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435 <option value="hg19" > hg19 </option>
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436 </param>
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437 <param name="initialview" type="text" size="100" value="1:0-100000" label="Chromosomal location to view when Dalliance starts" help="format: chromosome:start-end, no chr-prefix "/>
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438 <repeat name="gbtracks" title="Track" default="1" >
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439 <param name="item" type="data" label="file to display" help="Supported formats: bam, vcf, bed"/>
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440 <param name="gbfiletype" type="select" label="Select type of file" >
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441 <option value="vcfmemstore" > vcf </option>
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442 <option value="vcftabix" > vcf (large files) </option>
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443 <option value="bigbed" > bigBed </option>
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444 <option value="bedmemstore" > bed </option>
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445 <option value="bedtabix" > bed (large files)</option>
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446 <option value="bam" > bam (very large files not recommended) </option>
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447 </param>
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448 <param name="tracklabel" type="text" size="100" value="mytrack" label="track label" help="give your track a name">
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449 <sanitizer>
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450 <valid initial="default">
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451 <add preset="string.printable"/>
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parents: 6
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452 <remove value=" "/>
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parents: 6
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453 <remove value="("/>
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454 <remove value=")"/>
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455 </valid>
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456 <mapping initial="none">
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457 <add source=" " target="==space=="/>
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parents: 6
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458 <add source=")" target="==bclose=="/>
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parents: 6
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459 <add source="(" target="==bopen=="/>
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saskia-hiltemann
parents: 6
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460 </mapping>
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461 </sanitizer>
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462 </param>
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463 </repeat>
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464 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?" help="Insert a line break to force next item to appear below this one. If unchecked, the browser will decide layout" />
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465 </when>
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466
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467 </conditional>
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468 </repeat>
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469 </repeat>
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470
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471
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472
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473 </inputs>
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474
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475 <outputs>
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476 <data format="html" name="report" label="iReport: ${label}"/>
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477 </outputs>
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478
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479 <help><![CDATA[
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480 ============
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481 iReport
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482 ============
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483
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484 iReport is a tool for the easy creation of HTML reports from Galaxy datasets. Ideal to use as final step in a pipeline to display all results in a single, interactive report.
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485
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486
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diff changeset
487 **What's new**
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488
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489 - MarkDown support
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490 - HTML content item type
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491 - Link to download entire iReport on cover page
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492
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493
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494
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saskia-hiltemann
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diff changeset
495 **How to use**
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496
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497 - Specify report title and cover image (url)
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498 - Add any number of named tabs
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499 - Add content items to each tab
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500
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501 1. Text Field
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502 2. Text File
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503 3. PDF File
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504 4. HTML File
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505 5. Table
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506 6. Image File
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507 7. Links (URL/dataset)
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508 8. Links to all files in an archive dataset
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509
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saskia-hiltemann
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diff changeset
510 **Example History**
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511
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512 http://galaxy-demo.trait-ctmm.cloudlet.sara.nl/u/saskia-hiltemann/h/gcc2014-ireport-about-ireport
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513
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514
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515
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517 ]]></help>
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518 </tool>