--- a/stringtie.xml	Wed Jul 27 09:28:15 2022 +0000
+++ b/stringtie.xml	Mon Oct 31 20:08:02 2022 +0000
@@ -11,6 +11,7 @@
     <expand macro="version_command" />
     <command><![CDATA[
 #import re
+#set $compressed = ("bam","cram")
 mkdir -p ./special_de_output/sample1/ &&
 
 ## Get Guide GTF/GFF if selected
@@ -34,12 +35,12 @@
         -E $input_options.error_splice
     #end if
 #else
-    #if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'bam':
-        strigtie '$input_options.input_bam_short' '$input_options.input_bam_long'
-    #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype == 'bam':
+    #if $input_options.input_bam_short.file_ext in $compressed and $input_options.input_bam_long.file_ext in $compressed:
+        stringtie '$input_options.input_bam_short' '$input_options.input_bam_long'
+    #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype in $compressed:
         samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
         && stringtie short_sorted.sam '$input_options.input_bam_long'
-    #else if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'sam':
+    #else if $input_options.input_bam_short.metadata.ftype in $compressed and $input_options.input_bam_long.metadata.ftype == 'sam':
         samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
         && stringtie'$input_options.input_bam_short' long_sorted.sam
     #else
@@ -143,15 +144,15 @@
                 <option value="mixed_reads">Mixed mode: short and long reads</option>
             </param>
             <when value="short_reads">
-                <param name="input_bam" type="data" format="sam,bam" label="Input short mapped reads" help="Input BAM/SAM file containing the short reads you want to assemble into transcripts"/>
+                <param name="input_bam" type="data" format="sam,bam,cram" label="Input short mapped reads" help="Input BAM/SAM/CRAM file containing the short reads you want to assemble into transcripts"/>
             </when>
             <when value="long_reads">
-                <param name="input_bam" type="data" format="sam,bam" label="Input long mapped reads" help="Input BAM/SAM file containing the long reads you want to assemble into transcripts"/>
+                <param name="input_bam" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM file containing the long reads you want to assemble into transcripts"/>
                 <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
             </when>
             <when value="mixed_reads">
-                <param name="input_bam_short" type="data" format="sam,bam" label="Input short mapped reads" help="Input BAM/SAM file containing the short reads you want to assemble into transcripts"/>
-                <param name="input_bam_long" type="data" format="sam,bam" label="Input long mapped reads" help="Input BAM/SAM file containing the long reads you want to assemble into transcripts"/>
+                <param name="input_bam_short" type="data" format="sam,bam,cram" label="Input short mapped reads" help="Input BAM/SAM/CRAM file containing the short reads you want to assemble into transcripts"/>
+                <param name="input_bam_long" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM file containing the long reads you want to assemble into transcripts"/>
                 <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
             </when>
         </conditional>
@@ -418,6 +419,20 @@
             </conditional>            
             <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
         </test>
+        <!-- Test cram input -->
+        <test expect_num_outputs="1">
+            <conditional name="input_options">
+                <param name="input_mode" value="mixed_reads"/>
+                <param name="input_bam_short" ftype="cram" value="stringtie_in.cram" />
+                <param name="input_bam_long" ftype="cram" value="stringtie_in.cram" />
+            </conditional>            
+            <output name="output_gtf" ftype="gtf">
+                <assert_contents>
+                    <has_text text="gi|251831106|ref|NC_012920.1|"/>
+                    <has_text text="StringTie version 2.2.1"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[