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comparison iReport.xml @ 7:0f2b740536fb draft

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Uploaded
author saskia-hiltemann
date Mon, 21 Aug 2017 09:16:07 -0400
parents 42076db43d42
children 86219e4aa239
comparison
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6:42076db43d42 7:0f2b740536fb
1 <tool id="iReport" name="iReport" version="1"> 1 <tool id="iReport" name="iReport" version="1">
2 2
3 <!-- Note to Galaxy Admins: 3 <!-- Note to Galaxy Admins:
4 This wrapper contains one hidden parameter with hardcoded server location, this is currently needed for dalliance genome browser to function correctly, 4 This wrapper contains one hidden parameter with hardcoded server location, this is currently needed for dalliance genome browser to function correctly,
5 please change this value as needed! (see below for parameter: <param name="localhost" type="hidden" value="https://bioninf-galaxian.erasmusmc.nl"/>) 5 please change this value as needed! (see below for parameter: <param name="localhost" type="hidden" value="https://bioninf-galaxian.erasmusmc.nl"/>)
6 --> 6 -->
7 7 <description> create an HTML report </description>
8 8
9 <description> create an HTML report </description> 9 <command><![CDATA[
10 10
11 <requirements> 11 #set $labelb64 = str($label).encode('base64').replace('\n','')
12 <requirement type="set_environment">REPOSITORY_PATH</requirement> 12 #set $coverimageb64 = str($coverimage).encode('base64').replace('\n','')
13 </requirements> 13
14 14 iReport.sh
15 <command interpreter="bash"> 15 --toolpath '$__tool_directory__'
16 16 --galaxypath ${report.files_path}
17 #set $labelb64 = str($label).encode('base64').replace('\n','') 17 --htmlout ${report}
18 #set $coverimageb64 = str($coverimage).encode('base64').replace('\n','') 18 --minwidth ${minwidth}
19 19 --coverimage -${coverimageb64}
20 iReport.sh 20 #for $i, $t in enumerate($tabs)
21 --toolpath \$REPOSITORY_PATH 21 #set $tabtitleb64 = str($t.tabtitle).encode('base64').replace('\n','')
22 --galaxypath ${report.files_path} 22 --tab ${tabtitleb64}
23 --htmlout ${report} 23 #for $j, $u in enumerate($t.content)
24 --minwidth ${minwidth} 24 #if $u.filetype.itemtype == "image"
25 --coverimage -${coverimageb64} 25 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.zoomlevel}:${u.filetype.zoomenable}:${u.filetype.align}"
26 #for $i, $t in enumerate($tabs) 26 #else if $u.filetype.itemtype == "table"
27 #set $tabtitleb64 = str($t.tabtitle).encode('base64').replace('\n','') 27 #if $u.filetype.collink.columnhyperlink == "Y"
28 --tab ${tabtitleb64} 28 --item "${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}"
29 #for $j, $u in enumerate($t.content) 29 #else
30 #if $u.filetype.itemtype == "image" 30 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.fancy}:N:${u.filetype.minw}:${u.filetype.minh}"
31 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.zoomlevel}:${u.filetype.zoomenable}:${u.filetype.align}" 31 #end if
32 #else if $u.filetype.itemtype == "table" 32 #else if $u.filetype.itemtype == "link"
33 #if $u.filetype.collink.columnhyperlink == "Y" 33 --item "${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}:${proxy}"
34 --item "${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}" 34 #else if $u.filetype.itemtype == "weblink"
35 #else 35 #set $itemb64 = str($u.filetype.item).encode('base64').replace('\n','')
36 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.fancy}:N:${u.filetype.minw}:${u.filetype.minh}" 36 #set $item2b64 = str($u.filetype.item2).encode('base64').replace('\n','')
37 #end if 37 --item "${t.tabtitle}:${u.filetype.itemtype}:${itemb64}:${u.filetype.break}:${item2b64}"
38 #else if $u.filetype.itemtype == "link" 38 #else if $u.filetype.itemtype == "text"
39 --item "${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}:${proxy}" 39 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"
40 #else if $u.filetype.itemtype == "weblink" 40 #else if $u.filetype.itemtype == "textfile"
41 #set $itemb64 = str($u.filetype.item).encode('base64').replace('\n','') 41 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"
42 #set $item2b64 = str($u.filetype.item2).encode('base64').replace('\n','') 42 #else if $u.filetype.itemtype == "htmlfile"
43 --item "${t.tabtitle}:${u.filetype.itemtype}:${itemb64}:${u.filetype.break}:${item2b64}" 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}"
44 #else if $u.filetype.itemtype == "text" 44 #else if $u.filetype.itemtype == "htmlpage"
45 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}" 45 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}"
46 #else if $u.filetype.itemtype == "textfile" 46 #else if $u.filetype.itemtype == "genomebrowser"
47 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}" 47 #set $itemb64 = str($u.filetype.initialview).encode('base64').replace('\n','')
48 #else if $u.filetype.itemtype == "htmlfile" 48 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.genomebuild}:${u.filetype.break}:${__app__.security.encode_id($report.id)}:${localhost}:${itemb64}"
49 --item "${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}" 49 --newgb "-"
50 #else if $u.filetype.itemtype == "htmlpage" 50 #for $k, $gb in enumerate($u.filetype.gbtracks)
51 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}" 51 --genomebrowsertrack ${gb.item}:${gb.tracklabel}:${gb.gbfiletype}
52 #else if $u.filetype.itemtype == "genomebrowser" 52 #end for
53 #set $itemb64 = str($u.filetype.initialview).encode('base64').replace('\n','') 53 #else
54 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.genomebuild}:${u.filetype.break}:${__app__.security.encode_id($report.id)}:${localhost}:${itemb64}" 54 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}"
55 --newgb "-" 55 #end if
56 #for $k, $gb in enumerate($u.filetype.gbtracks) 56 #end for
57 --genomebrowsertrack ${gb.item}:${gb.tracklabel}:${gb.gbfiletype} 57 #end for
58 #end for 58 --label ${labelb64}
59 #else 59
60 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}" 60 ]]></command>
61 #end if 61 <inputs>
62 #end for 62 <!-- this sucks, but need to hardcode where galaxy is running from for some components -->
63 #end for 63 <param name="localhost" type="hidden" value="https://bioinf-galaxian.erasmusmc.nl/galaxy">
64 --label ${labelb64} 64 <sanitizer>
65 65 <valid initial="default">
66 </command> 66 <add preset="string.printable"/>
67 67 <remove value=":"/>
68 <inputs> 68 </valid>
69 <!-- this sucks, but need to hardcode where galaxy is running from for some components --> 69 <mapping initial="none">
70 <param name="localhost" type="hidden" value="https://bioinf-galaxian.erasmusmc.nl/galaxy"> 70 <add source=":" target="==colon=="/>
71 <sanitizer> 71 </mapping>
72 <valid initial="default"> 72 </sanitizer>
73 <add preset="string.printable"/> 73 </param>
74 <remove value=":"/> 74 <param name="proxy" type="hidden" value="galaxy"/>
75 </valid> 75 <!-- /sucks -->
76 <mapping initial="none"> 76
77 <add source=":" target="==colon=="/> 77
78 </mapping> 78 <param name="label" type="text" size="100" label="Name of Report" >
79 </sanitizer> 79 <sanitizer>
80 </param> 80 <valid initial="default">
81 <param name="proxy" type="hidden" value="galaxy"/> 81 <add preset="string.printable"/>
82 <!-- /sucks --> 82 <remove value=":"/>
83 83 <remove value="$"/>
84 84 <remove value="~"/>
85 <param name="label" type="text" size="100" label="Name of Report" > 85 <remove value="("/>
86 <sanitizer> 86 <remove value=")"/>
87 <valid initial="default"> 87 <remove value="&lt;"/>
88 <add preset="string.printable"/> 88 <remove value="&gt;"/>
89 <remove value=":"/> 89 </valid>
90 <remove value="$"/> 90 <mapping initial="none">
91 <remove value="~"/> 91 <add source="&lt;" target="&amp;#60;"/>
92 <remove value="("/> 92 <add source="&gt;" target="&amp;#62;"/>
93 <remove value=")"/> 93 <add source=":" target="&amp;#58;"/>
94 <remove value="&lt;"/> 94 <add source="$" target="&amp;#36;"/>
95 <remove value="&gt;"/> 95 <add source="~" target="&amp;#126;"/>
96 </valid> 96 <add source=")" target="&amp;#41;"/>
97 <mapping initial="none"> 97 <add source="(" target="&amp;#40;"/>
98 <add source="&lt;" target="&amp;#60;"/> 98
99 <add source="&gt;" target="&amp;#62;"/> 99 </mapping>
100 <add source=":" target="&amp;#58;"/> 100 </sanitizer>
101 <add source="$" target="&amp;#36;"/> 101 <validator type="empty_field" />
102 <add source="~" target="&amp;#126;"/> 102 </param>
103 <add source=")" target="&amp;#41;"/> 103 <param name="coverimage" type="text" size="100" label="Link to cover image" help="Optional. A default image will be used if not specified">
104 <add source="(" target="&amp;#40;"/> 104 <sanitizer>
105 105 <valid initial="default">
106 </mapping> 106 <add preset="string.printable"/>
107 </sanitizer> 107 <remove value=" "/>
108 <validator type="empty_field" /> 108 <remove value=":"/>
109 </param> 109 <remove value="$"/>
110 <param name="coverimage" type="text" size="100" label="Link to cover image" help="Optional. A default image will be used if not specified"> 110 <remove value="~"/>
111 <sanitizer> 111 <remove value="("/>
112 <valid initial="default"> 112 <remove value=")"/>
113 <add preset="string.printable"/> 113 <remove value="&lt;"/>
114 <remove value=" "/> 114 <remove value="&gt;"/>
115 <remove value=":"/> 115 </valid>
116 <remove value="$"/> 116 <mapping initial="none">
117 <remove value="~"/> 117 <add source=" " target=""/>
118 <remove value="("/> 118 <add source="&lt;" target="&amp;#60;"/>
119 <remove value=")"/> 119 <add source="&gt;" target="&amp;#62;"/>
120 <remove value="&lt;"/> 120 <add source=":" target="&amp;#58;"/>
121 <remove value="&gt;"/> 121 <add source="$" target="&amp;#36;"/>
122 </valid> 122 <add source="~" target="&amp;#126;"/>
123 <mapping initial="none"> 123 <add source=")" target="&amp;#41;"/>
124 <add source=" " target=""/> 124 <add source="(" target="&amp;#40;"/>
125 <add source="&lt;" target="&amp;#60;"/> 125 </mapping>
126 <add source="&gt;" target="&amp;#62;"/> 126 </sanitizer>
127 <add source=":" target="&amp;#58;"/> 127 </param>
128 <add source="$" target="&amp;#36;"/> 128
129 <add source="~" target="&amp;#126;"/> 129 <param name="minwidth" type="integer" min="0" max="5000" value="1200" label="Width of page (in pixels)" />
130 <add source=")" target="&amp;#41;"/> 130 <repeat name="tabs" title="Tab" default="1" >
131 <add source="(" target="&amp;#40;"/> 131 <param name="tabtitle" type="text" size="50" label="Enter tab name">
132 </mapping> 132 <sanitizer>
133 </sanitizer> 133 <valid initial="default">
134 </param> 134 <add preset="string.printable"/>
135 135 <remove value=":"/>
136 <param name="minwidth" type="integer" min="0" max="5000" value="1200" label="Width of page (in pixels)" /> 136 <remove value=" "/>
137 <repeat name="tabs" title="Tab" default="1" > 137 <remove value="$"/>
138 <param name="tabtitle" type="text" size="50" label="Enter tab name"> 138 <remove value="~"/>
139 <sanitizer> 139 <remove value="&lt;"/>
140 <valid initial="default"> 140 <remove value="&gt;"/>
141 <add preset="string.printable"/> 141 <remove value="("/>
142 <remove value=":"/> 142 <remove value=")"/>
143 <remove value=" "/> 143 </valid>
144 <remove value="$"/> 144 <mapping initial="none">
145 <remove value="~"/> 145 <add source=":" target="&amp;#58;"/>
146 <remove value="&lt;"/> 146 <add source=" " target="&amp;#32;"/>
147 <remove value="&gt;"/> 147 <add source="$" target="&amp;#36;"/>
148 <remove value="("/> 148 <add source="~" target="&amp;#126;"/>
149 <remove value=")"/> 149 <add source=")" target="&amp;#41;"/>
150 </valid> 150 <add source="(" target="&amp;#40;"/>
151 <mapping initial="none"> 151 </mapping>
152 <add source=":" target="&amp;#58;"/> 152 </sanitizer>
153 <add source=" " target="&amp;#32;"/> 153 <validator type="empty_field" />
154 <add source="$" target="&amp;#36;"/> 154 </param>
155 <add source="~" target="&amp;#126;"/> 155 <repeat name="content" title="Content-Item" default="1">
156 <add source=")" target="&amp;#41;"/> 156 <conditional name="filetype">
157 <add source="(" target="&amp;#40;"/> 157 <param name="itemtype" type="select" label="Select Item Type" >
158 </mapping> 158 <option value="" > Please choose item type </option>
159 </sanitizer> 159 <option value="text" > Text Field </option>
160 <validator type="empty_field" /> 160 <option value="textfile" > Text File from history </option>
161 </param> 161 <option value="htmlfile"> HTML File from history </option>
162 <repeat name="content" title="Content-Item" default="1"> 162 <option value="htmlpage"> iFrame with HTML page from web </option>
163 <conditional name="filetype"> 163 <option value="image"> Image </option>
164 <param name="itemtype" type="select" label="Select Item Type" > 164 <option value="pdf" > PDF File </option>
165 <option value="" > Please choose item type </option> 165 <option value="table"> Table </option>
166 <option value="text" > Text Field </option> 166 <option value="link" > Link to Dataset </option>
167 <option value="textfile" > Text File from history </option> 167 <option value="links"> Links to Files in Archive Dataset </option>
168 <option value="htmlfile"> HTML File from history </option> 168 <option value="weblink" > Web link </option>
169 <option value="htmlpage"> iFrame with HTML page from web </option> 169 <option value="genomebrowser" > Genome Browser (beta) </option>
170 <option value="image"> Image </option> 170 <validator type="empty_field" />
171 <option value="pdf" > PDF File </option> 171 </param>
172 <option value="table"> Table </option> 172
173 <option value="link" > Link to Dataset </option> 173 <!--###########################
174 <option value="links"> Links to Files in Archive Dataset </option> 174 # Text Field #
175 <option value="weblink" > Web link </option> 175 ########################### -->
176 <option value="genomebrowser" > Genome Browser (beta) </option> 176 <when value="text">
177 <validator type="empty_field" /> 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"/>
178 </param> 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" >
179 179 <sanitizer>
180 <!--########################### 180 <valid initial="default">
181 # Text Field # 181 <add preset="string.printable"/>
182 ########################### --> 182 <remove value="\"/>
183 <when value="text"> 183 <remove value="/"/>
184 <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"/> 184 <remove value=","/>
185 <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" > 185 <remove value=":"/>
186 <sanitizer> 186 <remove value="~"/>
187 <valid initial="default"> 187 <remove value="&lt;"/>
188 <add preset="string.printable"/> 188 <remove value="&gt;"/>
189 <remove value="\"/> 189 <remove value="&apos;"/>
190 <remove value="/"/> 190 <remove value="&quot;"/>
191 <remove value=","/> 191 <remove value="&#xA;"/>
192 <remove value=":"/> 192 <remove value="&#xD;"/>
193 <remove value="~"/> 193 <remove value="&amp;"/>
194 <remove value="&lt;"/> 194 <remove value="&#x3a;"/>
195 <remove value="&gt;"/> 195 <remove value=" "/>
196 <remove value="&apos;"/> 196 <remove value="`"/>
197 <remove value="&quot;"/> 197 <remove value="$"/>
198 <remove value="&#xA;"/> 198 <remove value="|"/>
199 <remove value="&#xD;"/> 199 </valid>
200 <remove value="&amp;"/> 200 <mapping initial="none">
201 <remove value="&#x3a;"/> 201 <add source="\" target="\\"/>
202 <remove value=" "/> 202 <add source="/" target="==slash=="/>
203 <remove value="`"/> 203 <add source="&amp;" target="&amp;&amp;"/>
204 <remove value="$"/> 204 <add source="&#xA;" target="&amp;n"/>
205 <remove value="|"/> 205 <add source="&#xD;" target="&amp;r"/>
206 </valid> 206 <add source="&#x3a;" target="&amp;c"/>
207 <mapping initial="none"> 207 <add source=" " target="==space=="/>
208 <add source="\" target="\\"/> 208 <add source="," target="==comma=="/>
209 <add source="/" target="==slash=="/> 209 <add source="&lt;" target="==lt=="/>
210 <add source="&amp;" target="&amp;&amp;"/> 210 <add source="&gt;" target="==gt=="/>
211 <add source="&#xA;" target="&amp;n"/> 211 <add source="&apos;" target="==apos=="/>
212 <add source="&#xD;" target="&amp;r"/> 212 <add source="&quot;" target="==quote=="/>
213 <add source="&#x3a;" target="&amp;c"/> 213 <add source=":" target="&amp;#58;"/>
214 <add source=" " target="==space=="/> 214 <add source="`" target="==backtick=="/>
215 <add source="," target="==comma=="/> 215 <add source="$" target="==dollar=="/>
216 <add source="&lt;" target="==lt=="/> 216 <add source="|" target="==bar=="/>
217 <add source="&gt;" target="==gt=="/> 217 <add source="~" target="&amp;#126;"/>
218 <add source="&apos;" target="==apos=="/> 218 </mapping>
219 <add source="&quot;" target="==quote=="/> 219 </sanitizer>
220 <add source=":" target="&amp;#58;"/> 220 <validator type="empty_field" />
221 <add source="`" target="==backtick=="/> 221 </param>
222 <add source="$" target="==dollar=="/> 222 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?"/>
223 <add source="|" target="==bar=="/> 223 </when>
224 <add source="~" target="&amp;#126;"/> 224
225 </mapping> 225 <!--###########################
226 </sanitizer> 226 # Text File #
227 <validator type="empty_field" /> 227 ########################### -->
228 </param> 228 <when value="textfile">
229 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?"/> 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"/>
230 </when> 230 <param name="item" type="data" label="Text File" help="Text file to display verbatim"/>
231 231 <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"/>
232 <!--########################### 232 </when>
233 # Text File # 233
234 ########################### --> 234 <!--###########################
235 <when value="textfile"> 235 # HTML File #
236 <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"/> 236 ########################### -->
237 <param name="item" type="data" label="Text File" help="Text file to display verbatim"/> 237 <when value="htmlfile">
238 <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"/> 238 <param name="item" type="data" label="HTML File" help="Contents of html file will be displayed in an iframe"/>
239 </when> 239 <param name="ireport" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is the link another iReport?"/>
240 240 <param name="height" type="integer" min="0" max="500000" value="350" label="Height (in pixels)" help="Height of the iFrame displaying the html page"/>
241 <!--########################### 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"/>
242 # HTML File # 242 </when>
243 ########################### --> 243
244 <when value="htmlfile"> 244 <when value="htmlpage">
245 <param name="item" type="data" label="HTML File" help="Contents of html file will be displayed in an iframe"/> 245 <param name="item" type="text" label="URL" size="100" help="Contents of webpage will be displayed in an iframe">
246 <param name="ireport" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is the link another iReport?"/> 246 <sanitizer>
247 <param name="height" type="integer" min="0" max="500000" value="350" label="Height (in pixels)" help="Height of the iFrame displaying the html page"/> 247 <valid initial="default">
248 <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"/> 248 <add preset="string.printable"/>
249 </when> 249 <remove value="&amp;"/>
250 250 <remove value=":"/>
251 <when value="htmlpage"> 251 <remove value="/"/>
252 <param name="item" type="text" label="URL" size="100" help="Contents of webpage will be displayed in an iframe"> 252 <remove value=" "/>
253 <sanitizer> 253 <remove value="$"/>
254 <valid initial="default"> 254 <remove value="~"/>
255 <add preset="string.printable"/> 255 <remove value="("/>
256 <remove value="&amp;"/> 256 <remove value=")"/>
257 <remove value=":"/> 257 </valid>
258 <remove value="/"/> 258 <mapping initial="none">
259 <remove value=" "/> 259 <add source="&amp;" target="&amp;#38;"/>
260 <remove value="$"/> 260 <add source=":" target="&amp;#58;"/>
261 <remove value="~"/> 261 <add source="/" target="&amp;#47;"/>
262 <remove value="("/> 262 <add source=" " target="&amp;#32;"/>
263 <remove value=")"/> 263 <add source="$" target="&amp;#36;"/>
264 </valid> 264 <add source="~" target="&amp;#126;"/>
265 <mapping initial="none"> 265 <add source="~" target="&amp;#126;"/>
266 <add source="&amp;" target="&amp;#38;"/> 266 <add source=")" target="&amp;#41;"/>
267 <add source=":" target="&amp;#58;"/> 267 <add source="(" target="&amp;#40;"/>
268 <add source="/" target="&amp;#47;"/> 268 </mapping>
269 <add source=" " target="&amp;#32;"/> 269 </sanitizer>
270 <add source="$" target="&amp;#36;"/> 270 </param>
271 <add source="~" target="&amp;#126;"/> 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"/>
272 <add source="~" target="&amp;#126;"/> 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"/>
273 <add source=")" target="&amp;#41;"/> 273 </when>
274 <add source="(" target="&amp;#40;"/> 274
275 </mapping> 275 <!--###########################
276 </sanitizer> 276 # Images #
277 </param> 277 ########################### -->
278 <param name="height" type="integer" min="0" max="500000" value="350" label="Height (in pixels)" help="Height of the iFrame displaying the html page"/> 278 <when value="image">
279 <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"/> 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."/>
280 </when> 280 <param name="zoomlevel" type="integer" min="0" max="5000" value="250" label="Width (in pixels)" help="enter 0 to keep original size" />
281 281 <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"/>
282 <!--########################### 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." >
283 # Images # 283 <option value="none" > default (recommended) </option>
284 ########################### --> 284 <option value="left" > left </option>
285 <when value="image"> 285 <option value="right" > right </option>
286 <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."/> 286 <option value="middle"> center </option>
287 <param name="zoomlevel" type="integer" min="0" max="5000" value="250" label="Width (in pixels)" help="enter 0 to keep original size" /> 287 <!--<option value="top"> top </option>
288 <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"/> 288 <option value="bottom"> bottom </option>-->
289 <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." > 289 </param>
290 <option value="none" > default (recommended) </option> 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"/>
291 <option value="left" > left </option> 291 </when>
292 <option value="right" > right </option> 292
293 <option value="middle"> center </option> 293 <!--###########################
294 <!--<option value="top"> top </option> 294 # Table #
295 <option value="bottom"> bottom </option>--> 295 ########################### -->
296 </param> 296 <when value="table">
297 <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"/> 297 <param name="item" type="data" label="Table File" help="must be a tab-delimited file with a 1-line header" />
298 </when> 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)"/>
299 299 <param name="minw" type="integer" value="0" label="Minimum width of table (in pixels)" help="only needed when tables are not displaying correctly"/>
300 <!--########################### 300 <param name="minh" type="integer" value="0" label="Minimum height of table (in pixels)" help="only needed when tables are not displaying correctly"/>
301 # Table # 301 <conditional name="collink">
302 ########################### --> 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">
303 <when value="table"> 303 <option value="N"> No </option>
304 <param name="item" type="data" label="Table File" help="must be a tab-delimited file with a 1-line header" /> 304 <option value="Y"> Yes </option>
305 <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)"/> 305 </param>
306 <param name="minw" type="integer" value="0" label="Minimum width of table (in pixels)" help="only needed when tables are not displaying correctly"/> 306 <when value="Y">
307 <param name="minh" type="integer" value="0" label="Minimum height of table (in pixels)" help="only needed when tables are not displaying correctly"/> 307 <param name="urlcol" type="data_column" data_ref="item" multiple="False" label="Column to turn in to weblinks" />
308 <conditional name="collink"> 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=">
309 <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"> 309 <sanitizer>
310 <option value="N"> No </option> 310 <valid initial="default">
311 <option value="Y"> Yes </option> 311 <add preset="string.printable"/>
312 </param> 312 <remove value="&amp;"/>
313 <when value="Y"> 313 <remove value=":"/>
314 <param name="urlcol" type="data_column" data_ref="item" multiple="False" label="Column to turn in to weblinks" /> 314 <remove value="/"/>
315 <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="> 315 <remove value=" "/>
316 <sanitizer> 316 <remove value="~"/>
317 <valid initial="default"> 317 <remove value="("/>
318 <add preset="string.printable"/> 318 <remove value=")"/>
319 <remove value="&amp;"/> 319 </valid>
320 <remove value=":"/> 320 <mapping initial="none">
321 <remove value="/"/> 321 <add source="&amp;" target="==amp=="/>
322 <remove value=" "/> 322 <add source=":" target="==colon=="/>
323 <remove value="~"/> 323 <add source="/" target="//"/>
324 <remove value="("/> 324 <add source=" " target=""/>
325 <remove value=")"/> 325 <add source="~" target="&amp;#126;"/>
326 </valid> 326 <add source=")" target="&amp;#41;"/>
327 <mapping initial="none"> 327 <add source="(" target="&amp;#40;"/>
328 <add source="&amp;" target="==amp=="/> 328 </mapping>
329 <add source=":" target="==colon=="/> 329 </sanitizer>
330 <add source="/" target="//"/> 330 </param>
331 <add source=" " target=""/> 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">
332 <add source="~" target="&amp;#126;"/> 332 <sanitizer>
333 <add source=")" target="&amp;#41;"/> 333 <valid initial="default">
334 <add source="(" target="&amp;#40;"/> 334 <add preset="string.printable"/>
335 </mapping> 335 <remove value="&amp;"/>
336 </sanitizer> 336 <remove value="/"/>
337 </param> 337 <remove value=" "/>
338 <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"> 338 <remove value="~"/>
339 <sanitizer> 339 <remove value="("/>
340 <valid initial="default"> 340 <remove value=")"/>
341 <add preset="string.printable"/> 341 </valid>
342 <remove value="&amp;"/> 342 <mapping initial="none">
343 <remove value="/"/> 343 <add source="&amp;" target="&amp;&amp;"/>
344 <remove value=" "/> 344 <add source="/" target="//"/>
345 <remove value="~"/> 345 <add source=" " target=""/>
346 <remove value="("/> 346 <add source="~" target="&amp;#126;"/>
347 <remove value=")"/> 347 <add source=")" target="&amp;#41;"/>
348 </valid> 348 <add source="(" target="&amp;#40;"/>
349 <mapping initial="none"> 349 </mapping>
350 <add source="&amp;" target="&amp;&amp;"/> 350 </sanitizer>
351 <add source="/" target="//"/> 351 </param>
352 <add source=" " target=""/> 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"/>
353 <add source="~" target="&amp;#126;"/> 353 </when>
354 <add source=")" target="&amp;#41;"/> 354 </conditional>
355 <add source="(" target="&amp;#40;"/> 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"/>
356 </mapping> 356 </when>
357 </sanitizer> 357
358 </param> 358 <!--###########################
359 <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"/> 359 # PDF File #
360 </when> 360 ########################### -->
361 </conditional> 361 <when value="pdf">
362 <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"/> 362 <param name="item" type="data" label="PDF File" format="pdf"/>
363 </when> 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"/>
364 364 </when>
365 <!--########################### 365
366 # PDF File # 366 <!--###########################
367 ########################### --> 367 # Links #
368 <when value="pdf"> 368 ########################### -->
369 <param name="item" type="data" label="PDF File" format="pdf"/> 369 <when value="link">
370 <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"/> 370 <param name="item" type="data" label="File to link to" />
371 </when> 371 <param name="item2" type="text" size="100" label="link text" help="text to display as a link"/>
372 372 <param name="ireport" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is the link another iReport?"/>
373 <!--########################### 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"/>
374 # Links # 374 </when>
375 ########################### --> 375
376 <when value="link"> 376 <when value="links">
377 <param name="item" type="data" label="File to link to" /> 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"/>
378 <param name="item2" type="text" size="100" label="link text" help="text to display as a link"/> 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" />
379 <param name="ireport" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is the link another iReport?"/> 379 </when>
380 <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"/> 380
381 </when> 381 <when value="weblink">
382 382 <param name="item" type="text" size="100" label="web location to link to " help="url to link to">
383 <when value="links"> 383 <sanitizer>
384 <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"/> 384 <valid initial="default">
385 <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" /> 385 <add preset="string.printable"/>
386 </when> 386 <remove value=" "/>
387 387 <remove value="&lt;"/>
388 <when value="weblink"> 388 <remove value="&gt;"/>
389 <param name="item" type="text" size="100" label="web location to link to " help="url to link to"> 389 <remove value="~"/>
390 <sanitizer> 390 <remove value="("/>
391 <valid initial="default"> 391 <remove value=")"/>
392 <add preset="string.printable"/> 392 </valid>
393 <remove value=" "/> 393 <mapping initial="none">
394 <remove value="&lt;"/> 394 <add source=" " target=""/>
395 <remove value="&gt;"/> 395 <add source="&lt;" target="&amp;#60;"/>
396 <remove value="~"/> 396 <add source="&gt;" target="&amp;#62;"/>
397 <remove value="("/> 397 <add source=" " target="&amp;#32;"/>
398 <remove value=")"/> 398 <add source=")" target="&amp;#41;"/>
399 </valid> 399 <add source="(" target="&amp;#40;"/>
400 <mapping initial="none"> 400 </mapping>
401 <add source=" " target=""/> 401 </sanitizer>
402 <add source="&lt;" target="&amp;#60;"/> 402 </param>
403 <add source="&gt;" target="&amp;#62;"/> 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">
404 <add source=" " target="&amp;#32;"/> 404 <sanitizer>
405 <add source=")" target="&amp;#41;"/> 405 <valid initial="default">
406 <add source="(" target="&amp;#40;"/> 406 <add preset="string.printable"/>
407 </mapping> 407 <remove value="&lt;"/>
408 </sanitizer> 408 <remove value="&gt;"/>
409 </param> 409 <remove value="~"/>
410 <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"> 410 <remove value=" "/>
411 <sanitizer> 411 <remove value="("/>
412 <valid initial="default"> 412 <remove value=")"/>
413 <add preset="string.printable"/> 413 </valid>
414 <remove value="&lt;"/> 414 <mapping initial="none">
415 <remove value="&gt;"/> 415 <add source="&lt;" target="&amp;#60;"/>
416 <remove value="~"/> 416 <add source="&gt;" target="&amp;#62;"/>
417 <remove value=" "/> 417 <add source="~" target="&amp;#126;"/>
418 <remove value="("/> 418 <add source=" " target="&amp;#32;"/>
419 <remove value=")"/> 419 <add source=")" target="&amp;#41;"/>
420 </valid> 420 <add source="(" target="&amp;#40;"/>
421 <mapping initial="none"> 421 </mapping>
422 <add source="&lt;" target="&amp;#60;"/> 422 </sanitizer>
423 <add source="&gt;" target="&amp;#62;"/> 423 </param>
424 <add source="~" target="&amp;#126;"/> 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"/>
425 <add source=" " target="&amp;#32;"/> 425 </when>
426 <add source=")" target="&amp;#41;"/> 426
427 <add source="(" target="&amp;#40;"/> 427 <!--###########################
428 </mapping> 428 # Genome Browser #
429 </sanitizer> 429 ########################### -->
430 </param> 430 <when value="genomebrowser">
431 <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"/> 431 <!-- TODO: hardcoded server location needed for dalliance to function correctly! Change as needed! -->
432 </when> 432
433 433 <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 ">
434 <!--########################### 434 <option value="hg18" > hg18 </option>
435 # Genome Browser # 435 <option value="hg19" > hg19 </option>
436 ########################### --> 436 </param>
437 <when value="genomebrowser"> 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 "/>
438 <!-- TODO: hardcoded server location needed for dalliance to function correctly! Change as needed! --> 438 <repeat name="gbtracks" title="Track" default="1" >
439 439 <param name="item" type="data" label="file to display" help="Supported formats: bam, vcf, bed"/>
440 <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 "> 440 <param name="gbfiletype" type="select" label="Select type of file" >
441 <option value="hg18" > hg18 </option> 441 <option value="vcfmemstore" > vcf </option>
442 <option value="hg19" > hg19 </option> 442 <option value="vcftabix" > vcf (large files) </option>
443 </param> 443 <option value="bigbed" > bigBed </option>
444 <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 "/> 444 <option value="bedmemstore" > bed </option>
445 <repeat name="gbtracks" title="Track" default="1" > 445 <option value="bedtabix" > bed (large files)</option>
446 <param name="item" type="data" label="file to display" help="Supported formats: bam, vcf, bed"/> 446 <option value="bam" > bam (very large files not recommended) </option>
447 <param name="gbfiletype" type="select" label="Select type of file" > 447 </param>
448 <option value="vcfmemstore" > vcf </option> 448 <param name="tracklabel" type="text" size="100" value="mytrack" label="track label" help="give your track a name">
449 <option value="vcftabix" > vcf (large files) </option> 449 <sanitizer>
450 <option value="bigbed" > bigBed </option> 450 <valid initial="default">
451 <option value="bedmemstore" > bed </option> 451 <add preset="string.printable"/>
452 <option value="bedtabix" > bed (large files)</option> 452 <remove value=" "/>
453 <option value="bam" > bam (very large files not recommended) </option> 453 <remove value="("/>
454 </param> 454 <remove value=")"/>
455 <param name="tracklabel" type="text" size="100" value="mytrack" label="track label" help="give your track a name"> 455 </valid>
456 <sanitizer> 456 <mapping initial="none">
457 <valid initial="default"> 457 <add source=" " target="==space=="/>
458 <add preset="string.printable"/> 458 <add source=")" target="==bclose=="/>
459 <remove value=" "/> 459 <add source="(" target="==bopen=="/>
460 <remove value="("/> 460 </mapping>
461 <remove value=")"/> 461 </sanitizer>
462 </valid> 462 </param>
463 <mapping initial="none"> 463 </repeat>
464 <add source=" " target="==space=="/> 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" />
465 <add source=")" target="==bclose=="/> 465 </when>
466 <add source="(" target="==bopen=="/> 466
467 </mapping> 467 </conditional>
468 </sanitizer> 468 </repeat>
469 </param> 469 </repeat>
470 </repeat> 470
471 <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" /> 471
472 </when> 472
473 473 </inputs>
474 </conditional> 474
475 </repeat> 475 <outputs>
476 </repeat> 476 <data format="html" name="report" label="iReport: ${label}"/>
477 477 </outputs>
478 478
479 479 <help><![CDATA[
480 </inputs> 480 ============
481 481 iReport
482 <outputs> 482 ============
483 <data format="html" name="report" label="iReport: ${label}"/> 483
484 </outputs> 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.
485 485
486 <help> 486
487 ============ 487 **What's new**
488 iReport 488
489 ============ 489 - MarkDown support
490 490 - HTML content item type
491 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. 491 - Link to download entire iReport on cover page
492 492
493 493
494 **What's new** 494
495 495 **How to use**
496 - MarkDown support 496
497 - HTML content item type 497 - Specify report title and cover image (url)
498 - Link to download entire iReport on cover page 498 - Add any number of named tabs
499 499 - Add content items to each tab
500 500
501 501 1. Text Field
502 **How to use** 502 2. Text File
503 503 3. PDF File
504 - Specify report title and cover image (url) 504 4. HTML File
505 - Add any number of named tabs 505 5. Table
506 - Add content items to each tab 506 6. Image File
507 507 7. Links (URL/dataset)
508 1. Text Field 508 8. Links to all files in an archive dataset
509 2. Text File 509
510 3. PDF File 510 **Example History**
511 4. HTML File 511
512 5. Table 512 http://galaxy-demo.trait-ctmm.cloudlet.sara.nl/u/saskia-hiltemann/h/gcc2014-ireport-about-ireport
513 6. Image File 513
514 7. Links (URL/dataset) 514
515 8. Links to all files in an archive dataset 515
516 516
517 **Example History** 517 ]]></help>
518
519 http://galaxy-demo.trait-ctmm.cloudlet.sara.nl/u/saskia-hiltemann/h/gcc2014-ireport-about-ireport
520
521
522
523
524 </help>
525 </tool> 518 </tool>