# HG changeset patch
# User saskia-hiltemann
# Date 1447691260 18000
# Node ID 1f44fe63e356046bc822d19492fff3826a6f872b
# Parent 0fe3b1e6d9c6d9ac204b20e411ab16dd6c7596a0
Uploaded
diff -r 0fe3b1e6d9c6 -r 1f44fe63e356 iReport.xml~
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/iReport.xml~ Mon Nov 16 11:27:40 2015 -0500
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+ create an HTML report
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+ REPOSITORY_PATH
+ datatables
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+
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+ #set $labelb64 = str($label).encode('base64').replace('\n','')
+ #set $coverimageb64 = str($coverimage).encode('base64').replace('\n','')
+
+ iReport.sh
+ --toolpath \$REPOSITORY_PATH
+ --galaxypath ${report.files_path}
+ --htmlout ${report}
+ --minwidth ${minwidth}
+ --coverimage -${coverimageb64}
+ #for $i, $t in enumerate($tabs)
+ #set $tabtitleb64 = str($t.tabtitle).encode('base64').replace('\n','')
+ --tab ${tabtitleb64}
+ #for $j, $u in enumerate($t.content)
+ #if $u.filetype.itemtype == "image"
+ --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.zoomlevel}:${u.filetype.zoomenable}:${u.filetype.align}"
+ #else if $u.filetype.itemtype == "table"
+ #if $u.filetype.collink.columnhyperlink == "Y"
+ --item "${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}"
+ #else
+ --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.fancy}:N:${u.filetype.minw}:${u.filetype.minh}"
+ #end if
+ #else if $u.filetype.itemtype == "link"
+ --item "${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}"
+ #else if $u.filetype.itemtype == "weblink"
+ #set $itemb64 = str($u.filetype.item).encode('base64').replace('\n','')
+ #set $item2b64 = str($u.filetype.item2).encode('base64').replace('\n','')
+ --item "${t.tabtitle}:${u.filetype.itemtype}:${itemb64}:${u.filetype.break}:${item2b64}"
+ #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}:${__app__.security.encode_id($u.filetype.item.id)}:${u.filetype.ireport}:${localhost}:${proxy}"
+ #else if $u.filetype.itemtype == "htmlpage"
+ --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}"
+ #else if $u.filetype.itemtype == "genomebrowser"
+ #set $itemb64 = str($u.filetype.initialview).encode('base64').replace('\n','')
+ --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.genomebuild}:${u.filetype.break}:${__app__.security.encode_id($report.id)}:${localhost}:${itemb64}"
+ --newgb "-"
+ #for $k, $gb in enumerate($u.filetype.gbtracks)
+ --genomebrowsertrack ${gb.item}:${gb.tracklabel}:${gb.gbfiletype}
+ #end for
+ #else
+ --item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}"
+ #end if
+ #end for
+ #end for
+ --label ${labelb64}
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+ ============
+ 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
+
+
+
+
+
+
diff -r 0fe3b1e6d9c6 -r 1f44fe63e356 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Nov 16 11:09:50 2015 -0500
+++ b/tool_dependencies.xml Mon Nov 16 11:27:40 2015 -0500
@@ -1,7 +1,7 @@
- $INSTALL_DIR
+ $REPOSITORY_INSTALL_DIR