command line parameters edition

ui/nG6/pi1/analyzes/AnalysisTemplate.tpl

@@ -53,6 +53,22 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 					<li class="parameter">{$analyse.params}</li>
 				</ul>
 				{/block}
+				
+				{block name=command_line_content}
+					{if $is_project_admin }
+					<br/>
+					<br/>
+					<div class="editable-block">
+						<span class="editable-block-head label label-info">Command</span>
+						<i>{$analyse.software}</i>
+						<span class="editable editable-block-content" 
+							id="editable-command-line" data-pk="{$analyze_id}" 
+							data-url="index.php?eID=tx_nG6&type=update_db_field&table=tx_nG6_analyze&field=params" data-type="textarea" >
+							{$analyse.params}
+						</span>
+					</div>
+					{/if}
+				{/block}
 			{/block}
 		</div>
 		{/if}

ui/nG6/pi1/analyzes/FastQC.tpl

@@ -17,7 +17,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 {extends file='AnalysisTemplate.tpl'}
 
-{block name=params}
+{block name=params_content}
 	{assign var="params" value=" "|explode:$analyse.params}
 	<ul>
 	{if in_array("--casava", $params)}

ui/nG6/pi1/class.tx_nG6_pi1.php

@@ -338,6 +338,7 @@ class tx_nG6_pi1 extends tslib_pibase {
 			$analysis_size = tx_nG6_db::get_analysis_size($this->piVars['analyze_id']);
 			$smarty->assign('analyse_size', tx_nG6_utils::get_octet_string_representation($analysis_size));
 			$smarty->assign('data_folder', $this->conf["data"]);
+			$smarty->assign('analyze_id', $this->piVars['analyze_id']);
 			
 			// Then select analyse results
 			$results = tx_nG6_db::select_analyse_results($this->piVars['analyze_id']);		

ui/nG6/res/css/tx_nG6.css

@@ -235,8 +235,29 @@ td.editable:hover {
 	cursor: text;
 	background-color: #f0f2f2 !important;
 }
-span.editable:hover {
-	/*border-bottom: 1px dashed #52A8EC;*/
+
+.editable-block {
+	position : relative;
+	padding : 10px 5px 10px 5px;
+	background-color: white ;
+	border:1px solid lightgrey;
+	border-radius:5px;
+	font-weight: bold;
+}
+.editable-block:hover{
+	cursor: text;
+	border: 1px dashed #52A8EC;
+	background-color: #f0f2f2 !important;
+}
+
+.editable-block-head{
+	position :absolute;
+	top:-15px;
+}
+
+.editable-block-content:hover{
+	cursor: text;
+	background-color: #f0f2f2 !important;
 }
 
 /* tx-nG-pi6 plugin style */
@@ -294,4 +315,4 @@ div#chart_options{
 	fill: none;
 	stroke: #ccc;
 	stroke-width: 1.5px;
-}
\ No newline at end of file
+}

ui/nG6/res/js/tx_nG6_pi1_analysis.js

@@ -54,6 +54,15 @@ function modal_height(substract, min) {
 }
 
 $(function () {
+	
+	// Grab relevant info from URL fragment
+    var params = simpleQueryParams(location.href),
+    	active_tab =  params["active_tab"];
+
+	if (active_tab) {
+		$('#myTab a[href="#'+active_tab+'"]').tab('show');
+	}
+	
     $(".file-display").each(function(i){
     	$(this).attr("id", "file_display_"+i);
     	var id = "file_display_"+i;
@@ -181,6 +190,28 @@ $(function () {
 	  	}
   	});
   	
+    // init editable 
+    $('.editable-block .editable-block-content').editable({
+    	toggle: 'manual'
+    });
+    
+    $('.editable-block').click(function(e){
+    	e.stopPropagation();
+    	$(this).children('.editable-block-content').editable('option', 'container', 'body');
+    	$(this).children('.editable-block-content').editable('option', 'success', function() {
+			location.assign(location.href+"&active_tab=parameters");
+ 	   	});
+    	$(this).children('.editable-block-content').editable('show');
+    });
+    $('.editable-block-content').click(function(e){
+    	e.stopPropagation();
+    	$(this).editable('option', 'success', function() {
+			location.assign(location.href+"&active_tab=parameters");
+ 	   	});
+    	$(this).editable('option', 'container', 'body');
+    	$(this).editable('show');
+    })
+    
     // Add numeric with white space in sort
 	jQuery.extend( jQuery.fn.dataTableExt.oSort, {
 		"numeric-pre": function ( a ) {
@@ -195,5 +226,5 @@ $(function () {
 		"numeric-desc": function ( a, b ) {
 			return b - a;
 		}
-	});   
+	});
 });

workflows/components/splitbc.py

@@ -105,7 +105,7 @@ class Splitbc (Analysis):
     def define_analysis(self):
         self.name = "Demultiplexing"
         self.description = "demultiplexing samples"
-        self.software = "Splitbc"
+        self.software = os.path.basename(self.get_exec_path("splitbc.pl"))
         self.options = [ "--bcfile", self.barcode_file ]
         
         if self.bol :