# HG changeset patch # User saskia-hiltemann # Date 1447687840 18000 # Node ID 88c8b1ffddac9291234cefc119d8107fcb1b86e6 # Parent ccba6130af2af3de55d1821769afbe3f4d8d9477 Uploaded diff -r ccba6130af2a -r 88c8b1ffddac iReport.xml --- a/iReport.xml Mon Nov 16 10:29:27 2015 -0500 +++ b/iReport.xml Mon Nov 16 10:30:40 2015 -0500 @@ -8,8 +8,9 @@ create an HTML report - + REPOSITORY_PATH + datatables diff -r ccba6130af2a -r 88c8b1ffddac iReport.xml~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/iReport.xml~ Mon Nov 16 10:30:40 2015 -0500 @@ -0,0 +1,525 @@ + + + + + + create an HTML report + + + REPOSITORY_PATH + + + + + #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} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ============ + 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 ccba6130af2a -r 88c8b1ffddac tool_dependencies.xml~ --- a/tool_dependencies.xml~ Mon Nov 16 10:29:27 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ - - - - $INSTALL_DIR - - - - tar xvf DataTables-1.9.4.tar - cp -R DataTables-1.9.4/ $INSTALL_DIR/ - - -