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comparison iReport.xml @ 4:a4813532bbc6 draft

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Added MarkDown support
author saskia-hiltemann
date Tue, 07 Oct 2014 08:41:30 -0400
parents e8755431a0cd
children 4e21ce709269
comparison
equal deleted inserted replaced
3:4a6ebda2a3ae 4:a4813532bbc6
1 <tool id="iReport" name="iReport" version="1"> 1 <tool id="iReport-dev" name="iReport-dev" version="1">
2 <description> create an HTML report </description> 2 <description> create an HTML report-dev </description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="set_environment">REPOSITORY_PATH</requirement> 5 <requirement type="set_environment">REPOSITORY_PATH</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="bash"> 7 <command interpreter="bash">
8 8 iReport.sh
9 iReport.sh
10 --toolpath \$REPOSITORY_PATH 9 --toolpath \$REPOSITORY_PATH
11 --galaxypath ${report.files_path} 10 --galaxypath ${report.files_path}
12 --htmlout ${report} 11 --htmlout ${report}
13 --minwidth ${minwidth} 12 --minwidth ${minwidth}
14 --coverimage "-${coverimage}" 13 --coverimage "-${coverimage}"
25 #end if 24 #end if
26 #else if $u.filetype.itemtype == "link" 25 #else if $u.filetype.itemtype == "link"
27 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${__app__.security.encode_id($u.filetype.item.id)}:${u.filetype.ireport}:${u.filetype.item2}" 26 --item "${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}"
28 #else if $u.filetype.itemtype == "weblink" 27 #else if $u.filetype.itemtype == "weblink"
29 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.item2}" 28 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.item2}"
29 #else if $u.filetype.itemtype == "text"
30 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"
31 #else if $u.filetype.itemtype == "textfile"
32 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"
33 #else if $u.filetype.itemtype == "htmlfile"
34 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}"
30 #else 35 #else
31 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}" 36 --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}"
32 #end if 37 #end if
33 #end for 38 #end for
34 #end for 39 #end for
35 --label "${label}" 40 --label "${label}"
36 </command> 41 </command>
37 42
38 <inputs> 43 <inputs>
39 <param name="label" type="text" size="100" label="Name of Report" /> 44 <param name="label" type="text" size="100" label="Name of Report" >
45 <validator type="empty_field" />
46 </param>
40 <param name="coverimage" type="text" size="100" label="Link to cover image" help="Optional. A default image will be used if not specified"/> 47 <param name="coverimage" type="text" size="100" label="Link to cover image" help="Optional. A default image will be used if not specified"/>
41 <param name="minwidth" type="integer" min="0" max="5000" value="1200" label="Width of page (in pixels)" /> 48 <param name="minwidth" type="integer" min="0" max="5000" value="1200" label="Width of page (in pixels)" />
42 <repeat name="tabs" title="Tab" default="1" > 49 <repeat name="tabs" title="Tab" default="1" >
43 <param name="tabtitle" type="text" size="50" label="Enter tab name"> 50 <param name="tabtitle" type="text" size="50" label="Enter tab name">
44 <sanitizer> 51 <sanitizer>
49 <remove value="&#xA;"/> 56 <remove value="&#xA;"/>
50 <remove value="&#xD;"/> 57 <remove value="&#xD;"/>
51 <remove value="&amp;"/> 58 <remove value="&amp;"/>
52 <remove value=":"/> 59 <remove value=":"/>
53 <remove value=" "/> 60 <remove value=" "/>
61 <remove value="`"/>
54 </valid> 62 </valid>
55 <mapping initial="none"> 63 <mapping initial="none">
56 <add source="\" target="\\"/> 64 <add source="\" target="\\"/>
57 <add source="&quot;" target="==quote=="/> 65 <add source="&quot;" target="==quote=="/>
58 <add source="&amp;" target="&amp;&amp;"/> 66 <add source="&amp;" target="&amp;&amp;"/>
59 <add source="&#xA;" target="&amp;n"/> 67 <add source="&#xA;" target="&amp;n"/>
60 <add source="&#xD;" target="&amp;r"/> 68 <add source="&#xD;" target="&amp;r"/>
61 <add source=":" target="==colon=="/> 69 <add source=":" target="==colon=="/>
62 <add source=" " target="_s_"/> 70 <add source=" " target="_s_"/>
71 <add source="`" target="==backtick=="/>
63 </mapping> 72 </mapping>
64 </sanitizer> 73 </sanitizer>
74 <validator type="empty_field" />
65 </param> 75 </param>
66 <repeat name="content" title="Content-Item" default="1"> 76 <repeat name="content" title="Content-Item" default="1">
67 <conditional name="filetype"> 77 <conditional name="filetype">
68 <param name="itemtype" type="select" label="Select Item Type" > 78 <param name="itemtype" type="select" label="Select Item Type" >
69 <option value="" > Please choose item type </option> 79 <option value="" > Please choose item type </option>
70 <option value="text" > Text Field </option> 80 <option value="text" > Text Field </option>
71 <option value="textfile" > Text File from history </option> 81 <option value="textfile" > Text File from history </option>
82 <option value="htmlfile"> HTML File from history </option>
72 <option value="image"> Image </option> 83 <option value="image"> Image </option>
73 <option value="pdf" > PDF File </option> 84 <option value="pdf" > PDF File </option>
74 <option value="table"> Table </option> 85 <option value="table"> Table </option>
75 <option value="link" > Link to file </option> 86 <option value="link" > Link to Dataset </option>
76 <option value="links"> Links to files in archive</option> 87 <option value="links"> Links to Files in Archive Dataset </option>
77 <option value="weblink" > Web link </option> 88 <option value="weblink" > Web link </option>
78 <validator type="empty_field" /> 89 <validator type="empty_field" />
79 </param> 90 </param>
80 <when value="text"> 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"/>
81 <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" > 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" >
82 <sanitizer> 94 <sanitizer>
83 <valid initial="default"> 95 <valid initial="default">
84 <add preset="string.printable"/> 96 <add preset="string.printable"/>
85 <remove value="\"/> 97 <remove value="\"/>
93 <remove value="&#xA;"/> 105 <remove value="&#xA;"/>
94 <remove value="&#xD;"/> 106 <remove value="&#xD;"/>
95 <remove value="&amp;"/> 107 <remove value="&amp;"/>
96 <remove value="&#x3a;"/> 108 <remove value="&#x3a;"/>
97 <remove value=" "/> 109 <remove value=" "/>
110 <remove value="`"/>
111 <remove value="$"/>
112 <remove value="|"/>
98 </valid> 113 </valid>
99 <mapping initial="none"> 114 <mapping initial="none">
100 <add source="\" target="\\"/> 115 <add source="\" target="\\"/>
101 <add source="/" target="==slash=="/> 116 <add source="/" target="==slash=="/>
102 <add source="&amp;" target="&amp;&amp;"/> 117 <add source="&amp;" target="&amp;&amp;"/>
108 <add source="&lt;" target="==lt=="/> 123 <add source="&lt;" target="==lt=="/>
109 <add source="&gt;" target="==gt=="/> 124 <add source="&gt;" target="==gt=="/>
110 <add source="&apos;" target="==apos=="/> 125 <add source="&apos;" target="==apos=="/>
111 <add source="&quot;" target="==quote=="/> 126 <add source="&quot;" target="==quote=="/>
112 <add source=":" target="==colon=="/> 127 <add source=":" target="==colon=="/>
128 <add source="`" target="==backtick=="/>
129 <add source="$" target="==dollar=="/>
130 <add source="|" target="==bar=="/>
113 </mapping> 131 </mapping>
114 </sanitizer> 132 </sanitizer>
133 <validator type="empty_field" />
115 </param> 134 </param>
116 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?"/> 135 <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?"/>
117 </when> 136 </when>
118 <when value="textfile"> 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"/>
119 <param name="item" type="data" label="Text File" help="Text file to display verbatim"/> 139 <param name="item" type="data" label="Text File" help="Text file to display verbatim"/>
120 <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"/> 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"/>
121 </when> 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>
122 <when value="image"> 147 <when value="image">
123 <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."/> 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."/>
124 <param name="zoomlevel" type="integer" min="0" max="5000" value="250" label="Width (in pixels)" help="enter 0 to keep original size" /> 149 <param name="zoomlevel" type="integer" min="0" max="5000" value="250" label="Width (in pixels)" help="enter 0 to keep original size" />
125 <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"/> 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"/>
126 <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." > 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." >
127 <option value="none" > default (recommended) </option> 152 <option value="none" > default (recommended) </option>
128 <option value="left" > left </option> 153 <option value="left" > left </option>
129 <option value="right" > right </option> 154 <option value="right" > right </option>
222 <outputs> 247 <outputs>
223 <data format="html" name="report" label="HTML report: ${label}"/> 248 <data format="html" name="report" label="HTML report: ${label}"/>
224 </outputs> 249 </outputs>
225 250
226 <help> 251 <help>
227 Description of tool for the users 252 ============
253 iReport
254 ============
255
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.
257
258
259 **What's new**
260
261 - MarkDown support
262 - HTML content item type
263 - Link to download entire iReport on cover page
264
265
266
267 **How to use**
268
269 - Specify report title and cover image (url)
270 - Add any number of named tabs
271 - Add content items to each tab
272
273 1. Text Field
274 2. Text File
275 3. PDF File
276 4. HTML File
277 5. Table
278 6. Image File
279 7. Links (URL/dataset)
280 8. Links to all files in an archive dataset
281
282 **Example History**
283
284 http://galaxy-demo.trait-ctmm.cloudlet.sara.nl/u/saskia-hiltemann/h/gcc2014-ireport-about-ireport
285
286
287
288
228 </help> 289 </help>
229 </tool> 290 </tool>