Mercurial > repos > saskia-hiltemann > ireport
diff iReport.xml @ 4:a4813532bbc6 draft
Added MarkDown support
| author | saskia-hiltemann |
|---|---|
| date | Tue, 07 Oct 2014 08:41:30 -0400 |
| parents | e8755431a0cd |
| children | 4e21ce709269 |
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--- a/iReport.xml Tue Sep 30 09:56:12 2014 -0400 +++ b/iReport.xml Tue Oct 07 08:41:30 2014 -0400 @@ -1,12 +1,11 @@ -<tool id="iReport" name="iReport" version="1"> - <description> create an HTML report </description> +<tool id="iReport-dev" name="iReport-dev" version="1"> + <description> create an HTML report-dev </description> <requirements> <requirement type="set_environment">REPOSITORY_PATH</requirement> </requirements> - <command interpreter="bash"> - - iReport.sh + <command interpreter="bash"> + iReport.sh --toolpath \$REPOSITORY_PATH --galaxypath ${report.files_path} --htmlout ${report} @@ -27,16 +26,24 @@ --item "${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}" #else if $u.filetype.itemtype == "weblink" --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.item2}" + #else if $u.filetype.itemtype == "text" + --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}" + #else if $u.filetype.itemtype == "textfile" + --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}" + #else if $u.filetype.itemtype == "htmlfile" + --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}" #else --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}" #end if #end for #end for --label "${label}" - </command> + </command> - <inputs> - <param name="label" type="text" size="100" label="Name of Report" /> + <inputs> + <param name="label" type="text" size="100" label="Name of Report" > + <validator type="empty_field" /> + </param> <param name="coverimage" type="text" size="100" label="Link to cover image" help="Optional. A default image will be used if not specified"/> <param name="minwidth" type="integer" min="0" max="5000" value="1200" label="Width of page (in pixels)" /> <repeat name="tabs" title="Tab" default="1" > @@ -51,6 +58,7 @@ <remove value="&"/> <remove value=":"/> <remove value=" "/> + <remove value="`"/> </valid> <mapping initial="none"> <add source="\" target="\\"/> @@ -60,8 +68,10 @@ <add source="
" target="&r"/> <add source=":" target="==colon=="/> <add source=" " target="_s_"/> + <add source="`" target="==backtick=="/> </mapping> </sanitizer> + <validator type="empty_field" /> </param> <repeat name="content" title="Content-Item" default="1"> <conditional name="filetype"> @@ -69,15 +79,17 @@ <option value="" > Please choose item type </option> <option value="text" > Text Field </option> <option value="textfile" > Text File from history </option> + <option value="htmlfile"> HTML File from history </option> <option value="image"> Image </option> <option value="pdf" > PDF File </option> <option value="table"> Table </option> - <option value="link" > Link to file </option> - <option value="links"> Links to files in archive</option> + <option value="link" > Link to Dataset </option> + <option value="links"> Links to Files in Archive Dataset </option> <option value="weblink" > Web link </option> <validator type="empty_field" /> </param> <when value="text"> + <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"/> <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" > <sanitizer> <valid initial="default"> @@ -95,6 +107,9 @@ <remove value="&"/> <remove value=":"/> <remove value=" "/> + <remove value="`"/> + <remove value="$"/> + <remove value="|"/> </valid> <mapping initial="none"> <add source="\" target="\\"/> @@ -110,18 +125,28 @@ <add source="'" target="==apos=="/> <add source=""" target="==quote=="/> <add source=":" target="==colon=="/> + <add source="`" target="==backtick=="/> + <add source="$" target="==dollar=="/> + <add source="|" target="==bar=="/> </mapping> </sanitizer> + <validator type="empty_field" /> </param> <param name="break" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Insert break after item?"/> </when> <when value="textfile"> + <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"/> <param name="item" type="data" label="Text File" help="Text file to display verbatim"/> <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"/> </when> + <when value="htmlfile"> + <param name="item" type="data" label="HTML File" help="Contents of html file will be displayed in an iframe"/> + <param name="height" type="integer" min="0" max="500000" value="350" label="Height (in pixels)" help="Height of the iFrame displaying the html page"/> + <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"/> + </when> <when value="image"> <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."/> - <param name="zoomlevel" type="integer" min="0" max="5000" value="250" label="Width (in pixels)" help="enter 0 to keep original size" /> + <param name="zoomlevel" type="integer" min="0" max="5000" value="250" label="Width (in pixels)" help="enter 0 to keep original size" /> <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"/> <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." > <option value="none" > default (recommended) </option> @@ -224,6 +249,42 @@ </outputs> <help> - Description of tool for the users +============ +iReport +============ + +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. + + +**What's new** + +- MarkDown support +- HTML content item type +- Link to download entire iReport on cover page + + + +**How to use** + +- Specify report title and cover image (url) +- Add any number of named tabs +- Add content items to each tab + +1. Text Field +2. Text File +3. PDF File +4. HTML File +5. Table +6. Image File +7. Links (URL/dataset) +8. Links to all files in an archive dataset + +**Example History** + +http://galaxy-demo.trait-ctmm.cloudlet.sara.nl/u/saskia-hiltemann/h/gcc2014-ireport-about-ireport + + + + </help> </tool>