Replace '.ext ==' pattern with is_of_type

Author: mvdbeek

tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml

@@ -8,9 +8,9 @@
         <![CDATA[
         zcat -f < '$input' | fastq_quality_filter -q $quality -p $percent -v -o '$output'
         ## fastqsanger uses offset 33, illumina and solexa offset 64 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217/table/T1/)
-        #if $input.ext == "fastqsanger":
+        #if $input.is_of_type(fastqsanger):
             -Q 33
-        #elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
+        #elif $input.is_of_type(fastqillumina" or $input.is_of_type(fastqsolexa):
             -Q 64
         #end if
         ]]>

tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml

@@ -7,9 +7,9 @@
     <command>
         <![CDATA[
         gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v
-        #if $input.ext == "fastqsanger":
+        #if $input.is_of_type('fastqsanger'):
             -Q 33
-        #elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
+        #elif $input.is_of_type('fastqillumina') or $input.is_of_type('fastqsolexa'):
             -Q 64
         #end if
         ]]>

tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml

@@ -7,9 +7,9 @@
     <command>
         <![CDATA[
         zcat -f < '$input' | fastx_artifacts_filter -v -o '$output'
-        #if $input.ext == "fastqsanger":
+        #if $input.is_of_type('fastqsanger'):
             -Q 33
-        #elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
+        #elif $input.is_of_type('fastqillumina') or $input.is_of_type('fastqsolexa'):
             -Q 64
         #end if
         ]]>

tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml

@@ -7,9 +7,9 @@
     <command>
         <![CDATA[
         zcat -f < '$input' | fastx_clipper -l $minlength -a '$clip_source.clip_sequence' -d $keepdelta -o '$output' -v $KEEP_N $DISCARD_OPTIONS
-        #if $input.ext == "fastqsanger":
+        #if $input.is_of_type('fastqsanger'):
             -Q 33
-        #elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
+        #elif $input.is_of_type('fastqillumina') or $input.is_of_type('fastqsolexa'):
             -Q 64
         #end if
         ]]>

tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml

@@ -7,9 +7,9 @@
     <command>
         <![CDATA[
         zcat -f < '$input' | fastx_collapser -v -o '$output'
-        #if $input.ext == "fastqsanger":
+        #if $input.is_of_type('fastqsanger'):
             -Q 33
-        #elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
+        #elif $input.is_of_type('fastqillumina') or $input.is_of_type('fastqsolexa'):
             -Q 64
         #end if
         ]]>

tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml

@@ -7,9 +7,9 @@
     <command>
         <![CDATA[
         zcat -f < '$input' | fastx_quality_stats -o '$output'
-        #if $input.ext == "fastqsanger":
+        #if $input.is_of_type('fastqsanger'):
             -Q 33
-        #elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
+        #elif $input.is_of_type('fastqillumina') or $input.is_of_type('fastqsolexa'):
             -Q 64
         #end if
         ]]>

tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml

@@ -7,9 +7,9 @@
     <command>
         <![CDATA[
         zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v
-        #if $input.ext == "fastqsanger":
+        #if $input.is_of_type('fastqsanger'):
             -Q 33
-        #elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
+        #elif $input.is_of_type('fastqillumina') or $input.is_of_type('fastqsolexa'):
             -Q 64
         #end if
         ]]>

tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml

@@ -7,9 +7,9 @@
     <command>
         <![CDATA[
         zcat -f < '$input' | fastx_reverse_complement -v -o '$output'
-        #if $input.ext == "fastqsanger":
+        #if $input.is_of_type('fastqsanger'):
             -Q 33
-        #elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
+        #elif $input.is_of_type('fastqillumina') or $input.is_of_type('fastqsolexa'):
             -Q 64
         #end if
         ]]>

tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml

@@ -7,9 +7,9 @@
     <command>
         <![CDATA[
         zcat -f < '$input' | fastx_trimmer -v -f $first -l $last -o '$output'
-        #if $input.ext == "fastqsanger":
+        #if $input.is_of_type('fastqsanger'):
             -Q 33
-        #elif $input.ext == "fastqillumina" or $input.ext == "fastqsolexa":
+        #elif $input.is_of_type('fastqillumina') or $input.is_of_type('fastqsolexa'):
             -Q 64
         #end if
         ]]>