mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-31 02:28:09 +08:00
Convert tool menu and edit attributes to mako.
This commit is contained in:
James Taylor
@@ -27,7 +27,7 @@ class RootController( BaseController ):
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@web.expose
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def tool_menu( self, trans ):
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return trans.fill_template('tool_menu.tmpl', toolbox=self.get_toolbox() )
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return trans.fill_template('/root/tool_menu.mako', toolbox=self.get_toolbox() )
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@web.expose
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def tool_help( self, trans, id ):
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@@ -265,7 +265,7 @@ class RootController( BaseController ):
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ldatatypes = [x for x in trans.app.datatypes_registry.datatypes_by_extension.iterkeys()]
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ldatatypes.sort()
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trans.log_event( "Opened edit view on dataset %s" % str(id) )
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return trans.fill_template( "edit_data.tmpl", data=data, metadata=metadata,
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return trans.fill_template( "/dataset/edit_attributes.mako", data=data, metadata=metadata,
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datatypes=ldatatypes, err=None )
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@web.expose
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@@ -0,0 +1,132 @@
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<%inherit file="/base.mako"/>
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<%def name="title()">Your saved histories</%def>
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<%def name="datatype( dataset, datatypes )">
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<select name="datatype">
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## $datatypes.sort()
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%for ext in datatypes:
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%if dataset.ext == ext:
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<option value="${ext}" selected="yes">${ext}</option>
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%else:
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<option value="${ext}">${ext}</option>
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%endif
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%endfor
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</select>
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</%def>
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<div class="toolForm">
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<div class="toolFormTitle">Edit Attributes</div>
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<div class="toolFormBody">
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<form name="edit_attributes" action="${h.url_for( action='edit' )}" method="post">
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<input type="hidden" name="id" value="${data.id}">
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<div class="form-row">
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<label>
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Name:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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<input type="text" name="name" value="${data.name}" size="40">
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</div>
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<div style="clear: both"></div>
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</div>
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<div class="form-row">
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<label>
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Info:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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<input type="text" name="info" value="${data.info}" size="40">
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</div>
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<div style="clear: both"></div>
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</div>
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%for element in metadata:
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<div class="form-row">
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<label>
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${element.spec.desc}:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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${element.get_html()}
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</div>
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<div style="clear: both"></div>
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</div>
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%endfor
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<div class="form-row">
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<input type="submit" name="save" value="Save">
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</div>
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</form>
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<form name="auto_detect" action="${h.url_for( action='edit' )}" method="post">
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<input type="hidden" name="id" value="${data.id}">
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<div style="float: left; width: 250px; margin-right: 10px;">
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<input type="submit" name="detect" value="Auto-detect">
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</div>
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<div class="toolParamHelp" style="clear: both;">
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This will inspect the dataset and attempt to correct the above column values
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if they are not accurate.
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</div>
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</form>
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</div>
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</div>
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<p />
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<% converters = data.get_converter_types() %>
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%if len( converters ) > 0:
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<div class="toolForm">
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<div class="toolFormTitle">Convert to new format</div>
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<div class="toolFormBody">
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<form name="convert_data" action="${h.url_for( action='edit' )}" method="post">
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<input type="hidden" name="id" value="${data.id}">
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<div class="form-row">
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<label>
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Convert to:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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<select name="target_type">
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%for key, value in converters.items():
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<option value="${key}">${value.name[8:]}</option>
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%endfor
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</select>
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</div>
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<div class="toolParamHelp" style="clear: both;">
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This will create a new dataset with the contents of this
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dataset converted to a new format.
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</div>
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<div style="clear: both"></div>
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</div>
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<div class="form-row">
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<input type="submit" name="convert_data" value="Convert">
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</div>
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</form>
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</div>
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</div>
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<p />
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%endif
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<div class="toolForm">
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<div class="toolFormTitle">Change data type</div>
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<div class="toolFormBody">
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<form name="change_datatype" action="${h.url_for( action='edit' )}" method="post">
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<input type="hidden" name="id" value="${data.id}">
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<div class="form-row">
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<label>
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New Type:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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${datatype( data, datatypes )}
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</div>
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<div class="toolParamHelp" style="clear: both;">
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This will change the datatype of the existing dataset
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but <i>not</i> modify its contents. Use this if Galaxy
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has incorrectly guessed the type of your dataset.
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</div>
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<div style="clear: both"></div>
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</div>
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<div class="form-row">
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<input type="submit" name="change" value="Save">
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</div>
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</form>
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</div>
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</div>
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@@ -1,148 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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#from galaxy.util.expressions import ExpressionContext
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<html>
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<head>
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<title>Galaxy</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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<link href="$h.url_for('/static/style/base.css')" rel="stylesheet" type="text/css" />
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</head>
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<body>
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#if $getVar( 'error_message', None )
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<div class="errormessagesmall">$error_message</div>
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<p></p>
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#end if
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#def datatype( $dataset, $datatypes )
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<select name="datatype">
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#$datatypes.sort()
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#for $ext in $datatypes:
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#if $dataset.ext == $ext
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<option value="$ext" selected="yes">$ext</option>
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#else
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<option value="$ext">$ext</option>
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#end if
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#end for
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</select>
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#end def
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<div class="toolForm">
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<div class="toolFormTitle">Edit Attributes</div>
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<div class="toolFormBody">
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<form name="edit_attributes" action="$h.url_for( action='edit' )" method="post">
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<input type="hidden" name="id" value="$data.id">
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<div class="form-row">
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<label>
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Name:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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<input type="text" name="name" value="$data.name" size="40">
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</div>
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<div style="clear: both"></div>
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</div>
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<div class="form-row">
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<label>
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Info:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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<input type="text" name="info" value="$data.info" size="40">
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</div>
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<div style="clear: both"></div>
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</div>
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#for $element in $metadata
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<div class="form-row">
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<label>
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${element.spec.desc}:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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$element.get_html()
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</div>
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<div style="clear: both"></div>
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</div>
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#end for
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<div class="form-row">
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<input type="submit" name="save" value="Save">
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</div>
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</form>
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<form name="auto_detect" action="$h.url_for( action='edit' )" method="post">
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<input type="hidden" name="id" value="$data.id">
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<div style="float: left; width: 250px; margin-right: 10px;">
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<input type="submit" name="detect" value="Auto-detect">
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</div>
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<div class="toolParamHelp" style="clear: both;">
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This will inspect the dataset and attempt to correct the above column values
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if they are not accurate.
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</div>
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</form>
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</div>
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</div>
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<p />
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#set $converters = $data.get_converter_types()
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#if len( $converters ) > 0:
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<div class="toolForm">
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<div class="toolFormTitle">Convert to new format</div>
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<div class="toolFormBody">
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<form name="convert_data" action="$h.url_for( action='edit' )" method="post">
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<input type="hidden" name="id" value="$data.id">
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<div class="form-row">
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<label>
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Convert to:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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<select name="target_type">
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#for $key, $value in $converters.items():
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<option value="$key">$value.name[8:]</option>
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#end for
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</select>
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</div>
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<div class="toolParamHelp" style="clear: both;">
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This will create a new dataset with the contents of this
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dataset converted to a new format.
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</div>
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<div style="clear: both"></div>
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</div>
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<div class="form-row">
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<input type="submit" name="convert_data" value="Convert">
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</div>
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</form>
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</div>
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</div>
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<p />
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#end if
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<div class="toolForm">
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<div class="toolFormTitle">Change data type</div>
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<div class="toolFormBody">
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<form name="change_datatype" action="$h.url_for( action='edit' )" method="post">
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<input type="hidden" name="id" value="$data.id">
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<div class="form-row">
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<label>
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New Type:
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</label>
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<div style="float: left; width: 250px; margin-right: 10px;">
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$datatype( $data, $datatypes )
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</div>
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<div class="toolParamHelp" style="clear: both;">
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This will change the datatype of the existing dataset
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but <i>not</i> modify its contents. Use this if Galaxy
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has incorrectly guessed the type of your dataset.
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</div>
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<div style="clear: both"></div>
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</div>
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<div class="form-row">
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<input type="submit" name="change" value="Save">
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</div>
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</form>
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</div>
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</div>
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</body>
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</html>
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@@ -0,0 +1,107 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<html>
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<head>
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<title>Galaxy Tools</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
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<link href="${h.url_for('/static/style/tool_menu.css')}" rel="stylesheet" type="text/css" />
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<script type="text/javascript" src="${h.url_for('/static/scripts/jquery.js')}"></script>
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<script type="text/javascript">
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var q = jQuery.noConflict();
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q(document).ready(function() {
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q( "div.toolSectionBody" ).hide();
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q( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" )
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var last_expanded = null;
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q( "div.toolSectionTitle" ).each( function() {
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var body = q(this).next( "div.toolSectionBody" );
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q(this).click( function() {
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if ( body.is( ":hidden" ) ) {
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if ( last_expanded ) last_expanded.slideUp( "fast" );
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last_expanded = body;
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body.slideDown( "fast" );
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}
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else {
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body.slideUp( "fast" );
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last_expanded = null;
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}
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});
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});
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q( "a[@minsizehint]" ).click( function() {
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if ( parent.handle_minwidth_hint ) {
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parent.handle_minwidth_hint( q(this).attr( "minsizehint" ) );
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}
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});
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});
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</script>
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</head>
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<body class="toolMenuPage">
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<div class="toolMenu">
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<div class="toolSectionList">
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%for i, section in enumerate( toolbox.sections ):
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%if i > 0:
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<div class="toolSectionPad"></div>
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%endif
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<div class="toolSectionTitle" id="title_${section.id}">
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<span>${section.name}</span>
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</div>
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<div id="${section.id}" class="toolSectionBody">
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<div class="toolSectionBg">
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%for tool in section.tools:
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%if not tool.hidden:
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<div class="toolTitle">
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<%
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if tool.input_required:
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link = h.url_for( 'tool_runner', tool_id=tool.id )
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else:
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link = h.url_for( tool.action, ** tool.get_static_param_values( t ) )
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%>
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## FIXME: This doesn't look right
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## %if "[[" in tool.description and "]]" in tool.description:
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## ${tool.description.replace( '[[', '<a href="link" target="galaxy_main">' % $tool.id ).replace( "]]", "</a>" )
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%if tool.name:
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<a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.name}</a> ${tool.description}
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%else:
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<a id="link-${tool.id}" href="${link}" target="galaxy_main" minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.description}</a>
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%endif
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</div>
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%endif
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%endfor
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</div>
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</div>
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%endfor
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## Link to workflow management. The location of this may change, but eventually
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## at least some workflows will appear here (the user should be able to
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## configure which of their stored workflows appear in the tools menu).
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%if app.config.enable_beta_features:
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<div class="toolSectionPad"></div>
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<div class="toolSectionPad"></div>
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<div class="toolSectionTitle" id="title_XXinternalXXworkflow">
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<span>Workflow <i>(beta)</i></span>
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</div>
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<div id="XXinternalXXworkflow" class="toolSectionBody">
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<div class="toolSectionBg">
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<div class="toolTitle">
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<a href="${h.url_for( controller='workflow', action='index' )}" target="galaxy_main">Manage</a> workflows
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</div>
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</div>
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</div>
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%endif
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</div>
|
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|
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</div>
|
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|
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<div style="height: 20px"></div>
|
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|
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</body>
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</html>
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@@ -1,29 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
|
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<html>
|
||||
|
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<head>
|
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<title>Share History</title>
|
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
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<link href="/static/style/base.css" rel="stylesheet" type="text/css" />
|
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</head>
|
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|
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<body>
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|
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<h2 align="center">Share history</h2>
|
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<p align="center">
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The link below can be used to the current history.
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</p>
|
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<p align="center">
|
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<b><a href="$url" target="_top"> $url</a></b>
|
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</p>
|
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<p>
|
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Send this link to others (right-click + copy link location) or bookmark it for further reference.
|
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</p>
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|
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<p>
|
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You may also create a new history by <b><a target="_top" href="$url&create=yes">clicking here</a></b>
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</p>
|
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|
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</body>
|
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|
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</html>
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@@ -1,134 +0,0 @@
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
|
||||
<html>
|
||||
|
||||
<head>
|
||||
<title>Galaxy Tools</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
||||
<link href="$h.url_for('/static/style/base.css')" rel="stylesheet" type="text/css" />
|
||||
<link href="$h.url_for('/static/style/tool_menu.css')" rel="stylesheet" type="text/css" />
|
||||
|
||||
<script type="text/javascript" src="$h.url_for('/static/scripts/jquery.js')"></script>
|
||||
|
||||
<script type="text/javascript">
|
||||
var q = jQuery.noConflict();
|
||||
q(document).ready(function() {
|
||||
q( "div.toolSectionBody" ).hide();
|
||||
q( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" )
|
||||
var last_expanded = null;
|
||||
q( "div.toolSectionTitle" ).each( function() {
|
||||
var body = q(this).next( "div.toolSectionBody" );
|
||||
q(this).click( function() {
|
||||
if ( body.is( ":hidden" ) ) {
|
||||
if ( last_expanded ) last_expanded.slideUp( "fast" );
|
||||
last_expanded = body;
|
||||
body.slideDown( "fast" );
|
||||
}
|
||||
else {
|
||||
body.slideUp( "fast" );
|
||||
last_expanded = null;
|
||||
}
|
||||
});
|
||||
});
|
||||
q( "a[@minsizehint]" ).click( function() {
|
||||
if ( parent.handle_minwidth_hint ) {
|
||||
parent.handle_minwidth_hint( q(this).attr( "minsizehint" ) );
|
||||
}
|
||||
});
|
||||
});
|
||||
</script>
|
||||
|
||||
<style type="text/css">
|
||||
#footer {
|
||||
/* Netscape 4, IE 4.x-5.0/Win and other lesser browsers will use this */
|
||||
position: absolute; left: 0px; bottom: 0px;
|
||||
}
|
||||
body > div#footer {
|
||||
/* used by Opera 5+, Netscape6+/Mozilla, Konqueror, Safari, OmniWeb 4.5+, iCab, ICEbrowser */
|
||||
position: fixed;
|
||||
}
|
||||
</style>
|
||||
|
||||
<!--[if gte IE 5.5]>
|
||||
<![if lt IE 7]>
|
||||
<style type="text/css">
|
||||
div#footer {
|
||||
/* IE5.5+/Win - this is more specific than the IE 5.0 version */
|
||||
width:110%;
|
||||
left: auto; bottom: auto;
|
||||
left:0px;
|
||||
lefta: expression( ( -0 - footer.offsetWidth + ( document.documentElement.clientWidth ? document.documentElement.clientWidth : document.body.clientWidth ) + ( ignoreMe2 = document.documentElement.scrollLeft ? document.documentElement.scrollLeft : document.body.scrollLeft ) ) + 'px' );
|
||||
top: expression( ( - footer.offsetHeight + ( document.documentElement.clientHeight ? document.documentElement.clientHeight : document.body.clientHeight ) + ( ignoreMe = document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop ) ) + 'px' );
|
||||
}
|
||||
</style>
|
||||
<![endif]>
|
||||
<![endif]-->
|
||||
|
||||
</head>
|
||||
|
||||
<body class="toolMenuPage">
|
||||
|
||||
<div class="toolMenu">
|
||||
|
||||
<div class="toolSectionList">
|
||||
#for $i, $section in enumerate( $toolbox.sections )
|
||||
#if $i > 0
|
||||
<div class="toolSectionPad"></div>
|
||||
#end if
|
||||
<div class="toolSectionTitle" id="title_$section.id">
|
||||
<span>$section.name</span>
|
||||
</div>
|
||||
<div id="$section.id" class="toolSectionBody">
|
||||
<div class="toolSectionBg">
|
||||
#for $tool in $section.tools
|
||||
#if not $tool.hidden:
|
||||
<div class="toolTitle">
|
||||
#if $tool.input_required
|
||||
#set $link = $h.url_for( 'tool_runner', tool_id=$tool.id )
|
||||
#else
|
||||
#set $link = $h.url_for( $tool.action, ** $tool.get_static_param_values( $t ) )
|
||||
#end if
|
||||
#if "[[" in $tool.description and "]]" in $tool.description
|
||||
$tool.description.replace( '[[', '<a href="$link" target="galaxy_main">' % $tool.id ).replace( "]]", "</a>" )
|
||||
#elif $tool.name
|
||||
<a id="link-$tool.id" href="$link" target="galaxy_main" minsizehint="$tool.uihints.get( 'minwidth', -1 )">$tool.name</a> $tool.description
|
||||
#else
|
||||
<a id="link-$tool.id" href="$link" target="galaxy_main" minsizehint="$tool.uihints.get( 'minwidth', -1 )">$tool.description</a>
|
||||
#end if
|
||||
</div>
|
||||
#end if
|
||||
#end for
|
||||
</div>
|
||||
</div>
|
||||
#end for
|
||||
|
||||
## Link to workflow management. The location of this may change, but eventually
|
||||
## at least some workflows will appear here (the user should be able to
|
||||
## configure which of their stored workflows appear in the tools menu).
|
||||
|
||||
#if $app.config.enable_beta_features
|
||||
<div class="toolSectionPad"></div>
|
||||
<div class="toolSectionPad"></div>
|
||||
<div class="toolSectionTitle" id="title_XXinternalXXworkflow">
|
||||
<span>Workflow <i>(beta)</i></span>
|
||||
</div>
|
||||
<div id="XXinternalXXworkflow" class="toolSectionBody">
|
||||
<div class="toolSectionBg">
|
||||
<div class="toolTitle">
|
||||
<a href="${h.url_for( controller='workflow', action='index' )}" target="galaxy_main">Manage</a> workflows
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
#end if
|
||||
|
||||
</div>
|
||||
|
||||
</div>
|
||||
|
||||
<div style="height: 20px"></div>
|
||||
|
||||
<div id="footer">
|
||||
<div class="footerheader"><b>Tools</b></div>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
</html>
|
||||
Reference in New Issue
Block a user