fix some templates;add docs

doc/user_guide.rst

@@ -93,7 +93,47 @@ Install an install module
 .. image:: ./images/bioGUI_graphmap.gif
    :scale: 50
 
+Use an install module
+---------------------
 
+After installing a software, e.g. graphmap, you can reload the list of available templates by pressing the reload button.
+
+Download the install module for graphmap as shown in the previous section.
+Next select the graphmap install module in the Install Templates template and fill out your *Linux User Password/sudo Password*. If you are on Windows, make sure that the *Use WSL?* checkbox is selected.
+
+.. image:: ./images/template_usage/graphmap_1.png
+    :scale: 50
+
+Enter the name of the template you would like to use in the input field within the *Store Template* group box (which you should have selected). In order for bioGUI to find a template it must reside in the *template* folder next to the bioGUI executable.
+Finally press *Install Program* and wait until the installation finishes.
+Besides the template being sent to bioGUI (in blue text), you should see the green message that your program has been installed correctly:
+
+.. image:: ./images/template_usage/graphmap_2.png
+    :scale: 50
+
+You can now *Reload* the templates again and will see a *graphmap* template on the left:
+
+.. image:: ./images/template_usage/graphmap_3.png
+    :scale: 50
+
+In this template you have to possibility to select the alignment mode (align or overlap/owler), specify the reference sequence, reads, gene annotation file (for splice-aware alignment) as well as the output file.
+To select files via a file dialog, click the corresponding button on the right.
+Using the *Additional Options* field, you can also enter command-line parameters directly.
+This may be necessary because the template is not complete, or new options have been added (or because you know shortcuts).
+
+Exemplarily we filled our some parameters:
+
+.. image:: ./images/template_usage/graphmap_4.png
+    :scale: 50
+
+Clicking on *Run Graphmap* will now execute graphmap via bioGUI. In this case, the called command-line tool is ``graphmap -r <reference> -d <reads> -o <output>``.
+
+Upon completion, the bioGUI options button (lower left) will become enabled again, as well as the *Run Graphmap* button. If you need to cancel the current process, click the *Cancel Run Graphmap* button.
+You will see all the intermediate output from graphmap and have the option to save the command-line output using the *Save log* button.
+If you want to save the inputs you made, using the *Save template* button of the bioGUI options, you can save the inputs you made. Save the template in the *template* directory in the same folder as bioGUI to see the template.
+
+.. image:: ./images/template_usage/graphmap_5.png
+    :scale: 50
 
 Adding Own Templates
 =====================

install_templates/install_graphmap.igui

@@ -192,27 +192,27 @@ $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">
+    <add id="args" sep=" ">
         <value from="\${graphmap_mode}"/>
-        <if comp="IS_SET" value1="\${graphmap_align_reference_rel}">
+        <if comp="IS_SET" value1="\${graphmap_align_reference_rel}"  sep=" ">
             <const>-r</const>
             <value from="\${graphmap_align_reference_rel}"/>
         </if>
 
-        <if comp="IS_SET" value1="\${graphmap_align_gtf}">
+        <if comp="IS_SET" value1="\${graphmap_align_gtf}" sep=" ">
             <const>--gtf</const>
             <value from="\${graphmap_align_gtf_rel}"/>
         </if>
 
-        <if comp="IS_SET" value1="\${graphmap_align_reads_rel}">
+        <if comp="IS_SET" value1="\${graphmap_align_reads_rel}" sep=" ">
             <const>-d</const>
             <value from="\${graphmap_align_reads_rel}"/>
         </if>        
 
 
         <value from="\${graphmap_options}"/>
 
-        <if comp="IS_SET" value1="\${graphmap_align_output_rel}">
+        <if comp="IS_SET" value1="\${graphmap_align_output_rel}" sep=" ">
             <const>-o</const>
             <value from="\${graphmap_align_output_rel}"/>
         </if>         

install_templates/install_hmmer.igui

@@ -41,7 +41,7 @@ if [ $# -gt 2 ]; then
 	if [ "$3" = "1" ]; then
 
 		if ! grep -q "$PROGDIRESC/$PROG" ~/.bashrc; then
-			echo "export PATH=\"$PROGDIRESC/$PROG:$PATH\" " >> ~/.bashrc;
+			echo "export PATH=\"$PROGDIRESC/$PROG:\$PATH\" " >> ~/.bashrc;
 		fi
 	fi
 

install_templates/install_mm_asm_racon.igui

@@ -255,7 +255,8 @@ $NCCMD <<EOF
 
     <relocate id="assembly_reads_rel" from="\${assembly_reads}" wsl="\${WSLsel}"/>
     <relocate id="assembly_dir_rel" from="\${assembly_dir}" wsl="\${WSLsel}"/>
-    <add id="args">
+
+    <add id="args" sep=" ">
 	<const>${APPBINARYDIR}/assemble.sh</const>
     <value from="\${assembly_reads_rel}"/>
     <value from="\${assembly_dir_rel}"/>

install_templates/install_rsem.igui

@@ -202,18 +202,18 @@ $NCCMD <<EOF
 <relocate id="rsem_calc_ref_name_rel" from="\${rsem_calc_ref_name}" wsl="\${WSLsel}"/>
 <relocate id="rsem_calc_sample_path_rel" from="\${rsem_calc_sample_path}" wsl="\${WSLsel}"/>
 
-<add id="rsem_calc_arguments">
+<add id="rsem_calc_arguments" sep=" ">
 <if comp="EQUAL" value1="rsem_calc_unpaired" value2="true">
 <value from="rsem_calc_unpaired_reads_rel"/>
 </if>
 
-<if comp="EQUAL" value1="rsem_calc_paired" value2="true">
+<if comp="EQUAL" value1="rsem_calc_paired" value2="true" sep=" ">
 <const>--paired-end</const>
 <value from="rsem_calc_paired_up_rel"/>
 <value from="rsem_calc_paired_down_rel"/>
 </if>
 
-<if comp="EQUAL" value1="rsem_calc_alignment" value2="true">
+<if comp="EQUAL" value1="rsem_calc_alignment" value2="true" sep=" ">
 <const>--alignments</const>
 <value from="rsem_calc_alignment_paired"/>
 <value from="rsem_calc_paired_up_rel"/>
@@ -229,7 +229,7 @@ $NCCMD <<EOF
 
 </add>
 
-<add id="rsem_calc_options">
+<add id="rsem_calc_options" sep=" ">
 <const>-p</const>
 <value from="rsem_calc_num_threads"/>
 

install_templates/install_trimmomatic.igui

@@ -284,8 +284,8 @@ $NCCMD <<EOF
         </if>
         <add sep=" " id="cl">
             <value from="files"/>
-            <add sep="">
-                <const>-threads </const>
+            <add sep=" ">
+                <const>-threads</const>
                 <value from="threads"/>
             </add>
             <add sep="">