update graphmap

mjoppich · Jul 13, 2019 · 226926e · 226926e
1 parent 6cc850b
commit 226926e
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Showing 4 changed files with 30 additions and 21 deletions.
diff --git a/install_templates/install_graphmap.igui b/install_templates/install_graphmap.igui
@@ -1,17 +1,16 @@
-#! Install graphmap (github)
+#! Install graphmap (github))
+
 
-if [ "$(uname)" == "Darwin" ]; then
-	source ~/.bash_profile
-else
-  echo ""
-fi
 
 if [ ! "$2" = "" ]; then
 
     if [ "$(uname)" == "Darwin" ]; then
 
         echo "Installing brew gcc"
-        brew install gcc@8
+        brew install gcc
+
+        alias gcc='gcc-8'
+        alias g++='g++-8'
 
     else
 
@@ -133,20 +132,23 @@ $NCCMD <<EOF
     <group title="Alignment Options">
 
 
-        <label>Program Mode (not all options used in all modes)</label>
+        <label>graphmap supports multiple modes:</label>
+        <label>the 'align' mode aligns reads to a reference</label>
+        <label>the 'owler' mode overlaps input sequences</label>
+        <label>Selected Program Mode (not all options used in all modes)</label>
         <combobox id="graphmap_mode" selected="align">
             <comboitem value="align">Alignment-Mode</comboitem>
             <comboitem value="owler">Overlap-Mode</comboitem>
         </combobox>
 
-        <label>Input Reference</label> <filedialog id="graphmap_align_reference" output="false">Select Input Reference (fa)</filedialog>
-        <label>Input Reads</label> <filedialog id="graphmap_align_reads" output="false">Select Input Reads (fq)</filedialog>
+        <label>Input Reference: the (reference) sequence to align to</label> <filedialog id="graphmap_align_reference" output="false">Select Input Reference (fa)</filedialog>
+        <label>Input Reads: the reads to align against the reference</label> <filedialog id="graphmap_align_reads" output="false">Select Input Reads (fq)</filedialog>
 
-        <label>Input Transcriptome</label> <filedialog id="graphmap_align_gtf" output="false">Select Input Annotation (gtf)</filedialog>
+        <label>Input Transcriptome (optional): gene annotation for transcriptomic align (considering exon structure)</label> <filedialog id="graphmap_align_gtf" output="false">Select Input Annotation (gtf)</filedialog>
 
-        <label>Alignment Output</label> <filedialog id="graphmap_align_output" output="true">Select Output Sam-File</filedialog>
+        <label>Alignment Output: location/filename of output file</label> <filedialog id="graphmap_align_output" output="true">Select Output Sam-File</filedialog>
 
-        <label>Alignment Algorithm</label>
+        <label>Alignment Algorithm to use (default: anchor):</label>
         <combobox id="graphmap_align_mode" selected="anchor">
             <comboitem value="anchor">Anchored alignment with end-to-end extension</comboitem>
             <comboitem value="anchorgotoh">Anchored alignment with Gotoh</comboitem>
@@ -155,7 +157,7 @@ $NCCMD <<EOF
 
         </combobox>
 
-        <label>Additional Options</label><input id="graphmap_options"></input>
+        <label >Additional Options (otional)</label><input id="graphmap_options"></input>
 
 
         <action program="graphmap" hint="click here to run program">Run Graphmap</action>  
@@ -189,27 +191,27 @@ $NCCMD <<EOF
     <relocate id="graphmap_align_gtf_rel" from="\${graphmap_align_gtf}" wsl="\${WSLsel}"/>
     <relocate id="graphmap_align_output_rel" from="\${graphmap_align_output}" wsl="\${WSLsel}"/>
 
-    <add id="args" sep=" ">
+    <add id="args">
         <value from="\${graphmap_mode}"/>
-        <if comp="IS_SET" value1="\${graphmap_align_reference_rel}"  sep=" ">
+        <if comp="IS_SET" value1="\${graphmap_align_reference_rel}">
             <const>-r</const>
             <value from="\${graphmap_align_reference_rel}"/>
         </if>
 
-        <if comp="IS_SET" value1="\${graphmap_align_gtf}" sep=" ">
+        <if comp="IS_SET" value1="\${graphmap_align_gtf}">
             <const>--gtf</const>
             <value from="\${graphmap_align_gtf_rel}"/>
         </if>
 
-        <if comp="IS_SET" value1="\${graphmap_align_reads_rel}" sep=" ">
+        <if comp="IS_SET" value1="\${graphmap_align_reads_rel}">
             <const>-d</const>
             <value from="\${graphmap_align_reads_rel}"/>
         </if>        
 
 
         <value from="\${graphmap_options}"/>
 
-        <if comp="IS_SET" value1="\${graphmap_align_output_rel}" sep=" ">
+        <if comp="IS_SET" value1="\${graphmap_align_output_rel}">
             <const>-o</const>
             <value from="\${graphmap_align_output_rel}"/>
         </if>         

diff --git a/src/parsing/visual_nodes/WindowWidgetStreamBoxNode.h b/src/parsing/visual_nodes/WindowWidgetStreamBoxNode.h
@@ -105,7 +105,6 @@ class WindowWidgetStreamBoxNode : public WindowWidgetNode {
 
             if (QCheckBox* pButton = dynamic_cast<QCheckBox*>(pChildElement))
             {
-                pButton->setChecked(true);
 
                 std::string sID = this->getAttribute(&oChildNode, "id", "");
                 if (sID.length() > 0)

diff --git a/src/parsing/visual_nodes/WindowWidgetStreamNode.h b/src/parsing/visual_nodes/WindowWidgetStreamNode.h
@@ -38,6 +38,7 @@ class WindowWidgetStreamNode : public WindowWidgetNode {
 
     }
 
+
     virtual CreatedElement getWindowElement( QDomElement* pDOMElement )
     {
 
@@ -47,6 +48,13 @@ class WindowWidgetStreamNode : public WindowWidgetNode {
 
         QCheckBox* pCheckbox = new QCheckBox(sValue);
 
+        bool bSelected = true;
+        if (this->getQAttribute(pDOMElement, "active", "").compare("FALSE", Qt::CaseInsensitive) == 0)
+        {
+            bSelected=false;
+        }
+        pCheckbox->setChecked(bSelected);
+
         oReturn.pElement = pCheckbox;
 
         return oReturn;

diff --git a/templates/WSL_install.gui b/templates/WSL_install.gui
@@ -38,7 +38,7 @@
     <streambox id="output1">
     <stream id="outputstream1">Normal Log</stream>
 	<stream id="outputstream2">Error Log</stream>
-	<stream id="savetemplate">Template</stream>
+	<stream id="savetemplate" active="false">Template</stream>
     </streambox>
 
   </vgroup>