| b'@@ -1,525 +1,518 @@\n <tool id="iReport" name="iReport" version="1">\n-\t\n-\t<!-- Note to Galaxy Admins:\n-\tThis wrapper contains one hidden parameter with hardcoded server location, this is currently needed for dalliance genome browser to function correctly,\n-\tplease change this value as needed! (see below for parameter: <param name="localhost" type="hidden" value="https://bioninf-galaxian.erasmusmc.nl"/>)\t\n-\t-->\n-\t\n-\t\n-\t<description> create an HTML report </description>\n-\t\n- <requirements>\n-\t\t<requirement type="set_environment">REPOSITORY_PATH</requirement>\n-\t</requirements>\n- \n-\t<command interpreter="bash"> \t\n-\t\t\n-\t\t#set $labelb64 = str($label).encode(\'base64\').replace(\'\\n\',\'\')\n-\t\t#set $coverimageb64 = str($coverimage).encode(\'base64\').replace(\'\\n\',\'\')\n-\t\t\n-\t\tiReport.sh \n-\t\t--toolpath \\$REPOSITORY_PATH\n-\t\t--galaxypath ${report.files_path}\n-\t\t--htmlout ${report}\n-\t\t--minwidth ${minwidth}\n-\t\t--coverimage -${coverimageb64}\n-\t\t#for $i, $t in enumerate($tabs)\n-\t\t#set $tabtitleb64 = str($t.tabtitle).encode(\'base64\').replace(\'\\n\',\'\')\n-\t\t--tab ${tabtitleb64}\n-\t\t#for $j, $u in enumerate($t.content)\n-\t\t#if $u.filetype.itemtype == "image"\n-\t\t--item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.zoomlevel}:${u.filetype.zoomenable}:${u.filetype.align}"\n-\t\t#else if $u.filetype.itemtype == "table"\n-\t\t#if $u.filetype.collink.columnhyperlink == "Y"\n-\t\t--item "${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}"\n-\t\t#else\n-\t\t--item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.fancy}:N:${u.filetype.minw}:${u.filetype.minh}"\n-\t\t#end if\n-\t\t#else if $u.filetype.itemtype == "link"\n-\t\t--item "${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}"\n-\t\t#else if $u.filetype.itemtype == "weblink"\n-\t\t#set $itemb64 = str($u.filetype.item).encode(\'base64\').replace(\'\\n\',\'\')\n-\t\t#set $item2b64 = str($u.filetype.item2).encode(\'base64\').replace(\'\\n\',\'\')\n-\t\t--item "${t.tabtitle}:${u.filetype.itemtype}:${itemb64}:${u.filetype.break}:${item2b64}"\n-\t\t#else if $u.filetype.itemtype == "text"\n-\t\t--item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"\n-\t\t#else if $u.filetype.itemtype == "textfile"\n-\t\t--item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.md}"\n-\t\t#else if $u.filetype.itemtype == "htmlfile"\n-\t\t--item "${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}"\n-\t\t#else if $u.filetype.itemtype == "htmlpage"\n-\t\t--item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}:${u.filetype.height}"\n-\t\t#else if $u.filetype.itemtype == "genomebrowser"\n-\t\t#set $itemb64 = str($u.filetype.initialview).encode(\'base64\').replace(\'\\n\',\'\')\n-\t\t--item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.genomebuild}:${u.filetype.break}:${__app__.security.encode_id($report.id)}:${localhost}:${itemb64}"\n-\t\t--newgb "-"\n-\t\t#for $k, $gb in enumerate($u.filetype.gbtracks)\n-\t\t--genomebrowsertrack ${gb.item}:${gb.tracklabel}:${gb.gbfiletype}\n-\t\t#end for\n-\t\t#else \n-\t\t--item "${t.tabtitle}:${u.filetype.itemtype}:${u.filetype.item}:${u.filetype.break}"\n-\t\t#end if\n-\t\t#end for\n-\t\t#end for\n-\t\t--label ${labelb64}\n-\t\t\n-\t</command>\n-\t\n-\t<inputs>\n-\t\t<!-- this sucks, but need to hardcode where galaxy is running from for some components -->\n-\t\t<param name="localhost" type="hidden" value="https://bioinf-galaxian.erasmusmc.nl/galaxy">\n-\t\t\t<sanitizer>\n-\t\t\t\t<valid initial="default"> \n-\t\t\t\t\t<add preset="string.printable"/> \n-'..b' # Genome Browser #\n+ ########################### -->\n+ <when value="genomebrowser">\n+ <!-- TODO: hardcoded server location needed for dalliance to function correctly! Change as needed! -->\n+\n+ <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 ">\n+ <option value="hg18" > hg18 </option>\n+ <option value="hg19" > hg19 </option>\n+ </param>\n+ <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 "/>\n+ <repeat name="gbtracks" title="Track" default="1" >\n+ <param name="item" type="data" label="file to display" help="Supported formats: bam, vcf, bed"/>\n+ <param name="gbfiletype" type="select" label="Select type of file" >\n+ <option value="vcfmemstore" > vcf </option>\n+ <option value="vcftabix" > vcf (large files) </option>\n+ <option value="bigbed" > bigBed </option>\n+ <option value="bedmemstore" > bed </option>\n+ <option value="bedtabix" > bed (large files)</option>\n+ <option value="bam" > bam (very large files not recommended) </option>\n+ </param>\n+ <param name="tracklabel" type="text" size="100" value="mytrack" label="track label" help="give your track a name">\n+ <sanitizer>\n+ <valid initial="default">\n+ <add preset="string.printable"/>\n+ <remove value=" "/>\n+ <remove value="("/>\n+ <remove value=")"/>\n+ </valid>\n+ <mapping initial="none">\n+ <add source=" " target="==space=="/>\n+ <add source=")" target="==bclose=="/>\n+ <add source="(" target="==bopen=="/>\n+ </mapping>\n+ </sanitizer>\n+ </param>\n+ </repeat>\n+ <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" />\n+ </when>\n+\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+\n+\n+\n+ </inputs>\n+\n+ <outputs>\n+ <data format="html" name="report" label="iReport: ${label}"/>\n+ </outputs>\n+\n+ <help><![CDATA[\n+============\n+iReport\n+============\n+\n+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.\n+\n+\n+**What\'s new**\n+\n+- MarkDown support\n+- HTML content item type\n+- Link to download entire iReport on cover page\n+\n+\n+\n+**How to use**\n+\n+- Specify report title and cover image (url)\n+- Add any number of named tabs\n+- Add content items to each tab\n+\n+1. Text Field\n+2. Text File\n+3. PDF File\n+4. HTML File\n+5. Table\n+6. Image File\n+7. Links (URL/dataset)\n+8. Links to all files in an archive dataset\n+\n+**Example History**\n+\n+http://galaxy-demo.trait-ctmm.cloudlet.sara.nl/u/saskia-hiltemann/h/gcc2014-ireport-about-ireport\n+\n+\n+\n+\n+ ]]></help>\n </tool>\n' |
