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comparison iReport.xml @ 6:42076db43d42 draft

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Fixed auto resizing plus various other minor bugs
author saskia-hiltemann
date Mon, 16 Nov 2015 08:56:22 -0500
parents 4e21ce709269
children 0f2b740536fb
comparison
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5:4e21ce709269 6:42076db43d42
1 <tool id="iReport" name="iReport" version="1"> 1 <tool id="iReport" name="iReport" version="1">
2 <description> create an HTML report </description> 2
3 3 <!-- Note to Galaxy Admins:
4 <requirements> 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"/>)
6 -->
7
8
9 <description> create an HTML report </description>
10
11 <requirements>
5 <requirement type="set_environment">REPOSITORY_PATH</requirement> 12 <requirement type="set_environment">REPOSITORY_PATH</requirement>
6 </requirements> 13 </requirements>
7 <command interpreter="bash"> 14
15 <command interpreter="bash">
16
17 #set $labelb64 = str($label).encode('base64').replace('\n','')
18 #set $coverimageb64 = str($coverimage).encode('base64').replace('\n','')
19
8 iReport.sh 20 iReport.sh
9 --toolpath \$REPOSITORY_PATH 21 --toolpath \$REPOSITORY_PATH
10 --galaxypath ${report.files_path} 22 --galaxypath ${report.files_path}
11 --htmlout ${report} 23 --htmlout ${report}
12 --minwidth ${minwidth} 24 --minwidth ${minwidth}
13 --coverimage "-${coverimage}" 25 --coverimage -${coverimageb64}
14 #for $i, $t in enumerate($tabs) 26 #for $i, $t in enumerate($tabs)
15 --tab ${t.tabtitle} 27 #set $tabtitleb64 = str($t.tabtitle).encode('base64').replace('\n','')
16 #for $j, $u in enumerate($t.content) 28 --tab ${tabtitleb64}
17 #if $u.filetype.itemtype == "image" 29 #for $j, $u in enumerate($t.content)
18 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.zoomlevel}:${u.filetype.zoomenable}:${u.filetype.align}" 30 #if $u.filetype.itemtype == "image"
19 #else if $u.filetype.itemtype == "table" 31 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.zoomlevel}:${u.filetype.zoomenable}:${u.filetype.align}"
20 #if $u.filetype.collink.columnhyperlink == "Y" 32 #else if $u.filetype.itemtype == "table"
21 --item "${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}" 33 #if $u.filetype.collink.columnhyperlink == "Y"
22 #else 34 --item "${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}"
23 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.fancy}:N" 35 #else
24 #end if 36 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.fancy}:N:${u.filetype.minw}:${u.filetype.minh}"
25 #else if $u.filetype.itemtype == "link" 37 #end if
26 --item "${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}" 38 #else if $u.filetype.itemtype == "link"
27 #else if $u.filetype.itemtype == "weblink" 39 --item "${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}:${proxy}"
28 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.item2}" 40 #else if $u.filetype.itemtype == "weblink"
29 #else if $u.filetype.itemtype == "text" 41 #set $itemb64 = str($u.filetype.item).encode('base64').replace('\n','')
30 --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','')
31 #else if $u.filetype.itemtype == "textfile" 43 --item "${t.tabtitle}:${u.filetype.itemtype}:${itemb64}:${u.filetype.break}:${item2b64}"
32 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}" 44 #else if $u.filetype.itemtype == "text"
33 #else if $u.filetype.itemtype == "htmlfile" 45 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"
34 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}" 46 #else if $u.filetype.itemtype == "textfile"
35 #else 47 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"
36 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}" 48 #else if $u.filetype.itemtype == "htmlfile"
37 #end if 49 --item "${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}"
38 #end for 50 #else if $u.filetype.itemtype == "htmlpage"
39 #end for 51 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}"
40 --label "${label}" 52 #else if $u.filetype.itemtype == "genomebrowser"
53 #set $itemb64 = str($u.filetype.initialview).encode('base64').replace('\n','')
54 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.genomebuild}:${u.filetype.break}:${__app__.security.encode_id($report.id)}:${localhost}:${itemb64}"
55 --newgb "-"
56 #for $k, $gb in enumerate($u.filetype.gbtracks)
57 --genomebrowsertrack ${gb.item}:${gb.tracklabel}:${gb.gbfiletype}
58 #end for
59 #else
60 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}"
61 #end if
62 #end for
63 #end for
64 --label ${labelb64}
65
41 </command> 66 </command>
67
68 <inputs>
69 <!-- this sucks, but need to hardcode where galaxy is running from for some components -->
70 <param name="localhost" type="hidden" value="https://bioinf-galaxian.erasmusmc.nl/galaxy">
71 <sanitizer>
72 <valid initial="default">
73 <add preset="string.printable"/>
74 <remove value=":"/>
75 </valid>
76 <mapping initial="none">
77 <add source=":" target="==colon=="/>
78 </mapping>
79 </sanitizer>
80 </param>
81 <param name="proxy" type="hidden" value="galaxy"/>
82 <!-- /sucks -->
83
84
85 <param name="label" type="text" size="100" label="Name of Report" >
86 <sanitizer>
87 <valid initial="default">
88 <add preset="string.printable"/>
89 <remove value=":"/>
90 <remove value="$"/>
91 <remove value="~"/>
92 <remove value="("/>
93 <remove value=")"/>
94 <remove value="&lt;"/>
95 <remove value="&gt;"/>
96 </valid>
97 <mapping initial="none">
98 <add source="&lt;" target="&amp;#60;"/>
99 <add source="&gt;" target="&amp;#62;"/>
100 <add source=":" target="&amp;#58;"/>
101 <add source="$" target="&amp;#36;"/>
102 <add source="~" target="&amp;#126;"/>
103 <add source=")" target="&amp;#41;"/>
104 <add source="(" target="&amp;#40;"/>
42 105
43 <inputs> 106 </mapping>
44 <param name="label" type="text" size="100" label="Name of Report" > 107 </sanitizer>
45 <validator type="empty_field" /> 108 <validator type="empty_field" />
46 </param> 109 </param>
47 <param name="coverimage" type="text" size="100" label="Link to cover image" help="Optional. A default image will be used if not specified"/> 110 <param name="coverimage" type="text" size="100" label="Link to cover image" help="Optional. A default image will be used if not specified">
111 <sanitizer>
112 <valid initial="default">
113 <add preset="string.printable"/>
114 <remove value=" "/>
115 <remove value=":"/>
116 <remove value="$"/>
117 <remove value="~"/>
118 <remove value="("/>
119 <remove value=")"/>
120 <remove value="&lt;"/>
121 <remove value="&gt;"/>
122 </valid>
123 <mapping initial="none">
124 <add source=" " target=""/>
125 <add source="&lt;" target="&amp;#60;"/>
126 <add source="&gt;" target="&amp;#62;"/>
127 <add source=":" target="&amp;#58;"/>
128 <add source="$" target="&amp;#36;"/>
129 <add source="~" target="&amp;#126;"/>
130 <add source=")" target="&amp;#41;"/>
131 <add source="(" target="&amp;#40;"/>
132 </mapping>
133 </sanitizer>
134 </param>
135
48 <param name="minwidth" type="integer" min="0" max="5000" value="1200" label="Width of page (in pixels)" /> 136 <param name="minwidth" type="integer" min="0" max="5000" value="1200" label="Width of page (in pixels)" />
49 <repeat name="tabs" title="Tab" default="1" > 137 <repeat name="tabs" title="Tab" default="1" >
50 <param name="tabtitle" type="text" size="50" label="Enter tab name"> 138 <param name="tabtitle" type="text" size="50" label="Enter tab name">
51 <sanitizer> 139 <sanitizer>
52 <valid initial="default"> 140 <valid initial="default">
53 <add preset="string.printable"/> 141 <add preset="string.printable"/>
54 <remove value="&quot;"/> 142 <remove value=":"/>
55 <remove value="\"/>
56 <remove value="&#xA;"/>
57 <remove value="&#xD;"/>
58 <remove value="&amp;"/>
59 <remove value=":"/>
60 <remove value=" "/> 143 <remove value=" "/>
61 <remove value="`"/> 144 <remove value="$"/>
145 <remove value="~"/>
146 <remove value="&lt;"/>
147 <remove value="&gt;"/>
148 <remove value="("/>
149 <remove value=")"/>
62 </valid> 150 </valid>
63 <mapping initial="none"> 151 <mapping initial="none">
64 <add source="\" target="\\"/> 152 <add source=":" target="&amp;#58;"/>
65 <add source="&quot;" target="==quote=="/> 153 <add source=" " target="&amp;#32;"/>
66 <add source="&amp;" target="&amp;&amp;"/> 154 <add source="$" target="&amp;#36;"/>
67 <add source="&#xA;" target="&amp;n"/> 155 <add source="~" target="&amp;#126;"/>
68 <add source="&#xD;" target="&amp;r"/> 156 <add source=")" target="&amp;#41;"/>
69 <add source=":" target="==colon=="/> 157 <add source="(" target="&amp;#40;"/>
70 <add source=" " target="_s_"/>
71 <add source="`" target="==backtick=="/>
72 </mapping> 158 </mapping>
73 </sanitizer> 159 </sanitizer>
74 <validator type="empty_field" /> 160 <validator type="empty_field" />
75 </param> 161 </param>
76 <repeat name="content" title="Content-Item" default="1"> 162 <repeat name="content" title="Content-Item" default="1">
77 <conditional name="filetype"> 163 <conditional name="filetype">
78 <param name="itemtype" type="select" label="Select Item Type" > 164 <param name="itemtype" type="select" label="Select Item Type" >
79 <option value="" > Please choose item type </option> 165 <option value="" > Please choose item type </option>
80 <option value="text" > Text Field </option> 166 <option value="text" > Text Field </option>
81 <option value="textfile" > Text File from history </option> 167 <option value="textfile" > Text File from history </option>
82 <option value="htmlfile"> HTML File from history </option> 168 <option value="htmlfile"> HTML File from history </option>
83 <option value="image"> Image </option> 169 <option value="htmlpage"> iFrame with HTML page from web </option>
84 <option value="pdf" > PDF File </option> 170 <option value="image"> Image </option>
85 <option value="table"> Table </option> 171 <option value="pdf" > PDF File </option>
86 <option value="link" > Link to Dataset </option> 172 <option value="table"> Table </option>
87 <option value="links"> Links to Files in Archive Dataset </option> 173 <option value="link" > Link to Dataset </option>
88 <option value="weblink" > Web link </option> 174 <option value="links"> Links to Files in Archive Dataset </option>
89 <validator type="empty_field" /> 175 <option value="weblink" > Web link </option>
90 </param> 176 <option value="genomebrowser" > Genome Browser (beta) </option>
91 <when value="text">
92 <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"/>
93 <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" >
94 <sanitizer>
95 <valid initial="default">
96 <add preset="string.printable"/>
97 <remove value="\"/>
98 <remove value="/"/>
99 <remove value=","/>
100 <remove value=":"/>
101 <remove value="&lt;"/>
102 <remove value="&gt;"/>
103 <remove value="&apos;"/>
104 <remove value="&quot;"/>
105 <remove value="&#xA;"/>
106 <remove value="&#xD;"/>
107 <remove value="&amp;"/>
108 <remove value="&#x3a;"/>
109 <remove value=" "/>
110 <remove value="`"/>
111 <remove value="$"/>
112 <remove value="|"/>
113 </valid>
114 <mapping initial="none">
115 <add source="\" target="\\"/>
116 <add source="/" target="==slash=="/>
117 <add source="&amp;" target="&amp;&amp;"/>
118 <add source="&#xA;" target="&amp;n"/>
119 <add source="&#xD;" target="&amp;r"/>
120 <add source="&#x3a;" target="&amp;c"/>
121 <add source=" " target="==space=="/>
122 <add source="," target="==comma=="/>
123 <add source="&lt;" target="==lt=="/>
124 <add source="&gt;" target="==gt=="/>
125 <add source="&apos;" target="==apos=="/>
126 <add source="&quot;" target="==quote=="/>
127 <add source=":" target="==colon=="/>
128 <add source="`" target="==backtick=="/>
129 <add source="$" target="==dollar=="/>
130 <add source="|" target="==bar=="/>
131 </mapping>
132 </sanitizer>
133 <validator type="empty_field" /> 177 <validator type="empty_field" />
134 </param>
135 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?"/>
136 </when>
137 <when value="textfile">
138 <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"/>
139 <param name="item" type="data" label="Text File" help="Text file to display verbatim"/>
140 <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"/>
141 </when>
142 <when value="htmlfile">
143 <param name="item" type="data" label="HTML File" help="Contents of html file will be displayed in an iframe"/>
144 <param name="height" type="integer" min="0" max="500000" value="350" label="Height (in pixels)" help="Height of the iFrame displaying the html page"/>
145 <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"/>
146 </when>
147 <when value="image">
148 <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."/>
149 <param name="zoomlevel" type="integer" min="0" max="5000" value="250" label="Width (in pixels)" help="enter 0 to keep original size" />
150 <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"/>
151 <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." >
152 <option value="none" > default (recommended) </option>
153 <option value="left" > left </option>
154 <option value="right" > right </option>
155 <option value="middle"> center </option>
156 <!--<option value="top"> top </option>
157 <option value="bottom"> bottom </option>-->
158 </param> 178 </param>
159 <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"/> 179
160 </when> 180 <!--###########################
161 <when value="table"> 181 # Text Field #
162 <param name="item" type="data" label="Table File" help="must be a tab-delimited file with a 1-line header" /> 182 ########################### -->
163 <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)"/> 183 <when value="text">
164 <conditional name="collink"> 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"/>
165 <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"> 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" >
166 <option value="N"> No </option> 186 <sanitizer>
167 <option value="Y"> Yes </option> 187 <valid initial="default">
188 <add preset="string.printable"/>
189 <remove value="\"/>
190 <remove value="/"/>
191 <remove value=","/>
192 <remove value=":"/>
193 <remove value="~"/>
194 <remove value="&lt;"/>
195 <remove value="&gt;"/>
196 <remove value="&apos;"/>
197 <remove value="&quot;"/>
198 <remove value="&#xA;"/>
199 <remove value="&#xD;"/>
200 <remove value="&amp;"/>
201 <remove value="&#x3a;"/>
202 <remove value=" "/>
203 <remove value="`"/>
204 <remove value="$"/>
205 <remove value="|"/>
206 </valid>
207 <mapping initial="none">
208 <add source="\" target="\\"/>
209 <add source="/" target="==slash=="/>
210 <add source="&amp;" target="&amp;&amp;"/>
211 <add source="&#xA;" target="&amp;n"/>
212 <add source="&#xD;" target="&amp;r"/>
213 <add source="&#x3a;" target="&amp;c"/>
214 <add source=" " target="==space=="/>
215 <add source="," target="==comma=="/>
216 <add source="&lt;" target="==lt=="/>
217 <add source="&gt;" target="==gt=="/>
218 <add source="&apos;" target="==apos=="/>
219 <add source="&quot;" target="==quote=="/>
220 <add source=":" target="&amp;#58;"/>
221 <add source="`" target="==backtick=="/>
222 <add source="$" target="==dollar=="/>
223 <add source="|" target="==bar=="/>
224 <add source="~" target="&amp;#126;"/>
225 </mapping>
226 </sanitizer>
227 <validator type="empty_field" />
228 </param>
229 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?"/>
230 </when>
231
232 <!--###########################
233 # Text File #
234 ########################### -->
235 <when value="textfile">
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"/>
237 <param name="item" type="data" label="Text File" help="Text file to display verbatim"/>
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"/>
239 </when>
240
241 <!--###########################
242 # HTML File #
243 ########################### -->
244 <when value="htmlfile">
245 <param name="item" type="data" label="HTML File" help="Contents of html file will be displayed in an iframe"/>
246 <param name="ireport" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is the link another iReport?"/>
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"/>
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"/>
249 </when>
250
251 <when value="htmlpage">
252 <param name="item" type="text" label="URL" size="100" help="Contents of webpage will be displayed in an iframe">
253 <sanitizer>
254 <valid initial="default">
255 <add preset="string.printable"/>
256 <remove value="&amp;"/>
257 <remove value=":"/>
258 <remove value="/"/>
259 <remove value=" "/>
260 <remove value="$"/>
261 <remove value="~"/>
262 <remove value="("/>
263 <remove value=")"/>
264 </valid>
265 <mapping initial="none">
266 <add source="&amp;" target="&amp;#38;"/>
267 <add source=":" target="&amp;#58;"/>
268 <add source="/" target="&amp;#47;"/>
269 <add source=" " target="&amp;#32;"/>
270 <add source="$" target="&amp;#36;"/>
271 <add source="~" target="&amp;#126;"/>
272 <add source="~" target="&amp;#126;"/>
273 <add source=")" target="&amp;#41;"/>
274 <add source="(" target="&amp;#40;"/>
275 </mapping>
276 </sanitizer>
277 </param>
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"/>
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"/>
280 </when>
281
282 <!--###########################
283 # Images #
284 ########################### -->
285 <when value="image">
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."/>
287 <param name="zoomlevel" type="integer" min="0" max="5000" value="250" label="Width (in pixels)" help="enter 0 to keep original size" />
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"/>
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." >
290 <option value="none" > default (recommended) </option>
291 <option value="left" > left </option>
292 <option value="right" > right </option>
293 <option value="middle"> center </option>
294 <!--<option value="top"> top </option>
295 <option value="bottom"> bottom </option>-->
168 </param> 296 </param>
169 <when value="Y"> 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"/>
170 <param name="urlcol" type="data_column" data_ref="item" multiple="False" label="Column to turn in to weblinks" /> 298 </when>
171 <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="> 299
300 <!--###########################
301 # Table #
302 ########################### -->
303 <when value="table">
304 <param name="item" type="data" label="Table File" help="must be a tab-delimited file with a 1-line header" />
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)"/>
306 <param name="minw" type="integer" value="0" label="Minimum width of table (in pixels)" help="only needed when tables are not displaying correctly"/>
307 <param name="minh" type="integer" value="0" label="Minimum height of table (in pixels)" help="only needed when tables are not displaying correctly"/>
308 <conditional name="collink">
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">
310 <option value="N"> No </option>
311 <option value="Y"> Yes </option>
312 </param>
313 <when value="Y">
314 <param name="urlcol" type="data_column" data_ref="item" multiple="False" label="Column to turn in to weblinks" />
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=">
316 <sanitizer>
317 <valid initial="default">
318 <add preset="string.printable"/>
319 <remove value="&amp;"/>
320 <remove value=":"/>
321 <remove value="/"/>
322 <remove value=" "/>
323 <remove value="~"/>
324 <remove value="("/>
325 <remove value=")"/>
326 </valid>
327 <mapping initial="none">
328 <add source="&amp;" target="==amp=="/>
329 <add source=":" target="==colon=="/>
330 <add source="/" target="//"/>
331 <add source=" " target=""/>
332 <add source="~" target="&amp;#126;"/>
333 <add source=")" target="&amp;#41;"/>
334 <add source="(" target="&amp;#40;"/>
335 </mapping>
336 </sanitizer>
337 </param>
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">
339 <sanitizer>
340 <valid initial="default">
341 <add preset="string.printable"/>
342 <remove value="&amp;"/>
343 <remove value="/"/>
344 <remove value=" "/>
345 <remove value="~"/>
346 <remove value="("/>
347 <remove value=")"/>
348 </valid>
349 <mapping initial="none">
350 <add source="&amp;" target="&amp;&amp;"/>
351 <add source="/" target="//"/>
352 <add source=" " target=""/>
353 <add source="~" target="&amp;#126;"/>
354 <add source=")" target="&amp;#41;"/>
355 <add source="(" target="&amp;#40;"/>
356 </mapping>
357 </sanitizer>
358 </param>
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"/>
360 </when>
361 </conditional>
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"/>
363 </when>
364
365 <!--###########################
366 # PDF File #
367 ########################### -->
368 <when value="pdf">
369 <param name="item" type="data" label="PDF File" format="pdf"/>
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"/>
371 </when>
372
373 <!--###########################
374 # Links #
375 ########################### -->
376 <when value="link">
377 <param name="item" type="data" label="File to link to" />
378 <param name="item2" type="text" size="100" label="link text" help="text to display as a link"/>
379 <param name="ireport" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is the link another iReport?"/>
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"/>
381 </when>
382
383 <when value="links">
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"/>
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" />
386 </when>
387
388 <when value="weblink">
389 <param name="item" type="text" size="100" label="web location to link to " help="url to link to">
390 <sanitizer>
391 <valid initial="default">
392 <add preset="string.printable"/>
393 <remove value=" "/>
394 <remove value="&lt;"/>
395 <remove value="&gt;"/>
396 <remove value="~"/>
397 <remove value="("/>
398 <remove value=")"/>
399 </valid>
400 <mapping initial="none">
401 <add source=" " target=""/>
402 <add source="&lt;" target="&amp;#60;"/>
403 <add source="&gt;" target="&amp;#62;"/>
404 <add source=" " target="&amp;#32;"/>
405 <add source=")" target="&amp;#41;"/>
406 <add source="(" target="&amp;#40;"/>
407 </mapping>
408 </sanitizer>
409 </param>
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">
411 <sanitizer>
412 <valid initial="default">
413 <add preset="string.printable"/>
414 <remove value="&lt;"/>
415 <remove value="&gt;"/>
416 <remove value="~"/>
417 <remove value=" "/>
418 <remove value="("/>
419 <remove value=")"/>
420 </valid>
421 <mapping initial="none">
422 <add source="&lt;" target="&amp;#60;"/>
423 <add source="&gt;" target="&amp;#62;"/>
424 <add source="~" target="&amp;#126;"/>
425 <add source=" " target="&amp;#32;"/>
426 <add source=")" target="&amp;#41;"/>
427 <add source="(" target="&amp;#40;"/>
428 </mapping>
429 </sanitizer>
430 </param>
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"/>
432 </when>
433
434 <!--###########################
435 # Genome Browser #
436 ########################### -->
437 <when value="genomebrowser">
438 <!-- TODO: hardcoded server location needed for dalliance to function correctly! Change as needed! -->
439
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 ">
441 <option value="hg18" > hg18 </option>
442 <option value="hg19" > hg19 </option>
443 </param>
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 "/>
445 <repeat name="gbtracks" title="Track" default="1" >
446 <param name="item" type="data" label="file to display" help="Supported formats: bam, vcf, bed"/>
447 <param name="gbfiletype" type="select" label="Select type of file" >
448 <option value="vcfmemstore" > vcf </option>
449 <option value="vcftabix" > vcf (large files) </option>
450 <option value="bigbed" > bigBed </option>
451 <option value="bedmemstore" > bed </option>
452 <option value="bedtabix" > bed (large files)</option>
453 <option value="bam" > bam (very large files not recommended) </option>
454 </param>
455 <param name="tracklabel" type="text" size="100" value="mytrack" label="track label" help="give your track a name">
172 <sanitizer> 456 <sanitizer>
173 <valid initial="default"> 457 <valid initial="default">
174 <add preset="string.printable"/> 458 <add preset="string.printable"/>
175 <remove value="&amp;"/>
176 <remove value=":"/>
177 <remove value="/"/>
178 <remove value=" "/> 459 <remove value=" "/>
460 <remove value="("/>
461 <remove value=")"/>
179 </valid> 462 </valid>
180 <mapping initial="none"> 463 <mapping initial="none">
181 <add source="&amp;" target="==amp=="/> 464 <add source=" " target="==space=="/>
182 <add source=":" target="==colon=="/> 465 <add source=")" target="==bclose=="/>
183 <add source="/" target="//"/> 466 <add source="(" target="==bopen=="/>
184 <add source=" " target=""/>
185 </mapping>
186 </sanitizer>
187 </param>
188 <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">
189 <sanitizer>
190 <valid initial="default">
191 <add preset="string.printable"/>
192 <remove value="&amp;"/>
193 <remove value="/"/>
194 <remove value=" "/>
195 </valid>
196 <mapping initial="none">
197 <add source="&amp;" target="&amp;&amp;"/>
198 <add source="/" target="//"/>
199 <add source=" " target=""/>
200 </mapping> 467 </mapping>
201 </sanitizer> 468 </sanitizer>
202 </param> 469 </param>
203 <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="zip,gz,bz2,tar"/> 470 </repeat>
204 </when> 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" />
205 </conditional> 472 </when>
206 <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"/> 473
207 </when> 474 </conditional>
208 <when value="pdf">
209 <param name="item" type="data" label="PDF File" format="pdf"/>
210 <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"/>
211 </when>
212 <when value="link">
213 <param name="item" type="data" label="File to link to" />
214 <param name="item2" type="text" size="100" label="link text" help="text to display as a link"/>
215 <param name="ireport" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is the link another iReport?"/>
216 <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"/>
217 </when>
218 <when value="links">
219 <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"/>
220 <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" />
221 </when>
222 <when value="weblink">
223 <param name="item" type="text" size="100" label="web location to link to " help="url to link to">
224 <sanitizer>
225 <valid initial="default">
226 <add preset="string.printable"/>
227 <remove value="&amp;"/>
228 <remove value=":"/>
229 </valid>
230 <mapping initial="none">
231 <add source="&amp;" target="==amp=="/>
232 <add source=":" target="==colon=="/>
233 </mapping>
234 </sanitizer>
235 </param>
236 <param name="item2" type="text" size="100" label="link text" help="text to display as a link"/>
237 <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 </when>
239 </conditional>
240 </repeat> 475 </repeat>
241 </repeat> 476 </repeat>
242 477
243 478
244 479
245 </inputs> 480 </inputs>
246 481
247 <outputs> 482 <outputs>
248 <data format="html" name="report" label="HTML report: ${label}"/> 483 <data format="html" name="report" label="iReport: ${label}"/>
249 </outputs> 484 </outputs>
250 485
251 <help> 486 <help>
252 ============ 487 ============
253 iReport 488 iReport
254 ============ 489 ============
255 490
256 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 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.
257 492
258 493
259 **What's new** 494 **What's new**
260 495
261 - MarkDown support 496 - MarkDown support
262 - HTML content item type 497 - HTML content item type
263 - Link to download entire iReport on cover page 498 - Link to download entire iReport on cover page
264 499
265 500
266 501
267 **How to use** 502 **How to use**
268 503
269 - Specify report title and cover image (url) 504 - Specify report title and cover image (url)
270 - Add any number of named tabs 505 - Add any number of named tabs
271 - Add content items to each tab 506 - Add content items to each tab
272 507
273 1. Text Field 508 1. Text Field
274 2. Text File 509 2. Text File
275 3. PDF File 510 3. PDF File
276 4. HTML File 511 4. HTML File
277 5. Table 512 5. Table
278 6. Image File 513 6. Image File
279 7. Links (URL/dataset) 514 7. Links (URL/dataset)
280 8. Links to all files in an archive dataset 515 8. Links to all files in an archive dataset
281 516
282 **Example History** 517 **Example History**
283 518
284 http://galaxy-demo.trait-ctmm.cloudlet.sara.nl/u/saskia-hiltemann/h/gcc2014-ireport-about-ireport 519 http://galaxy-demo.trait-ctmm.cloudlet.sara.nl/u/saskia-hiltemann/h/gcc2014-ireport-about-ireport
285 520
286 521
287 522
288 523
289 </help> 524 </help>
290 </tool> 525 </tool>