concoct fix linter errors

Author: bernt-matthias

tools/concoct/.lint_skip

@@ -70,11 +70,11 @@ concoct
                 <param name="total_percentage_pca" value="100"/>
                 <param name="seed" value="1"/>
                 <param name="iterations" value="500"/>
-                <param name="no_cov_normalization" value=""/>
+                <param name="no_cov_normalization" value="false"/>
             </section>
             <section name="output">
-                <param name="no_total_coverage" value=""/>
-                <param name="converge_out" value=""/>
+                <param name="no_total_coverage" value="false"/>
+                <param name="converge_out" value="false"/>
                 <param name="log" value="true"/>
             </section>
             <output name="process_log" ftype="txt" compare="contains">
@@ -113,11 +113,11 @@ concoct
                 <param name="total_percentage_pca" value="100"/>
                 <param name="seed" value="1"/>
                 <param name="iterations" value="500"/>
-                <param name="no_cov_normalization" value=""/>
+                <param name="no_cov_normalization" value="false"/>
             </section>
             <section name="output">
-                <param name="no_total_coverage" value=""/>
-                <param name="converge_out" value=""/>
+                <param name="no_total_coverage" value="false"/>
+                <param name="converge_out" value="false"/>
                 <param name="log" value="false"/>
             </section>
             <output name="output_pca_components" ftype="csv">

tools/concoct/concoct.xml

@@ -42,7 +42,7 @@ cut_up_fasta.py
             <param name="input_fasta" value="two_contigs.fa"/>
             <param name="chunk_size" value="1000" />
             <param name="overlap_size" value="0"/>
-            <param name="merge_last" value=""/>
+            <param name="merge_last" value="false"/>
             <param name="bedfile" value="false"/>
             <output name="output_fasta" ftype="fasta">
                 <assert_contents>
@@ -57,7 +57,7 @@ cut_up_fasta.py
             <param name="input_fasta" value="two_contigs.fa"/>
             <param name="chunk_size" value="1000" />
             <param name="overlap_size" value="0"/>
-            <param name="merge_last" value="--merge_last"/>
+            <param name="merge_last" value="true"/>
             <param name="bedfile" value="true"/>
             <output name="output_bed" ftype="bed">
                 <assert_contents>
@@ -79,7 +79,7 @@ cut_up_fasta.py
             <param name="input_fasta" value="composition.fa.gz" ftype="fasta.gz"/>
             <param name="chunk_size" value="500" />
             <param name="overlap_size" value="499"/>
-            <param name="merge_last" value=""/>
+            <param name="merge_last" value="false"/>
             <param name="bedfile" value="false"/>
             <output name="output_fasta" ftype="fasta">
                 <assert_contents>