--- a/yahs.xml	Tue Jul 12 06:39:08 2022 +0000
+++ b/yahs.xml	Wed Jul 27 09:26:18 2022 +0000
@@ -2,7 +2,7 @@
     <description>yet another HI-C scaffolding tool</description>
     <macros>
         <token name="@VERSION@">1.2a</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">yahs</requirement>
@@ -53,8 +53,11 @@
             #end if
             $function.no_contig_ec
             $function.no_scaffold_ec
-            -o yahs_out &&
-            ls -lah &&
+            -o yahs_out
+            #if $log_out
+                2> output.log
+            #end if
+            && ls -lah &&
             python '$__tool_directory__/move_files.py'
             && ls -lah ./*
         #else:
@@ -65,6 +68,9 @@
                 -l $function.length
             #end if
             -o output.fasta
+            #if $log_out:
+                2> output.log
+            #end if
         #end if
     ]]></command>
     <inputs>
@@ -85,11 +91,11 @@
                         The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual 
                         sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you 
                         use an enzyme-free prep, e.g. Omin-C.">
-                        <option value="not_especified">Not especified</option>
+                        <option value="not_specified">Not specified</option>
                         <option value="preconfigured">Preconfigured restriction enzymes</option>
                         <option value="specific">Enter a specific sequence</option>
                     </param>
-                    <when value="not_especified"/>
+                    <when value="not_specified"/>
                     <when value="preconfigured">
                         <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes">
                             <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
@@ -115,6 +121,7 @@
                 <param name="length" type='integer' label="Output fasta line length" value="60" min="1"/>
             </when>
         </conditional>
+        <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
     </inputs>
     <outputs>
         <!-- INITIAL ROUNDS -->
@@ -140,6 +147,9 @@
         <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta">
             <filter>function['function_select'] == "agp_to_fasta"</filter>
         </data>
+        <data format="txt" name="log_file" from_work_dir="output.log" label="${tool.name} ${on_string}, log file">
+            <filter>log_out</filter>
+        </data>
     </outputs>
     <tests>
         <test expect_num_outputs="5">
@@ -215,7 +225,25 @@
                 <param name="length" value="20"/>
             </conditional>
             <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>
-            <!-- COMMAND: agp_to_fasta teast.fasta test.agp -l 20 -o test_4 -->
+            <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 -->
+        </test>
+        <test expect_num_outputs="6">
+            <conditional name="function">
+                <param name="function_select" value="yahs"/>
+                <param name="fasta" value="test.fasta"/>
+                <param name="bfile" value="test.bed"/>
+                <param name="agp" value="test.agp"/>
+                <param name="res" value="50000,100000,150000,2000000,1000000"/>
+            </conditional>
+            <param name="log_out" value="yes"/>
+            <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/>
+            <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
+            <output name="log_file" ftype="txt">
+                <assert_contents>
+                    <has_text text="[I::main] CMD: yahs"/>
+                </assert_contents>
+            </output>
+            <!-- COMMAND:   yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
         </test>
     </tests>
     <help><![CDATA[