Add tsebra

tools/tsebra/tsebra.xml

@@ -23,12 +23,8 @@
         -c '$cfg_file'
     #end if
 
-    #if $ignore_transcrpts
-        --ignore_tx_phase
-    #end if
-    #if $filter_exon
-        --filter_single_exon_genes
-    #end if
+    $ignore_tx_phase
+    $filter_single_exon_genes
     #if $score_tab
         --score_tab '$output_tab'
     #end if 
@@ -42,8 +38,8 @@
         <param name="hint_file" argument="-e" type="data" format="gff" optional="true" label="List of files containing extrinsic evidence"/>
         <param name="cfg_file" argument="-c" type="data" format="txt" optional="true" label="Configuration file" help="Find the recommanded parameter at config/default.cfg"/>
         <param name="score_tab" argument="-s" type="boolean" checked="false" label="Print the transcript scores as a table to the specified file"/>
-        <param name="ignore_transcrpts" type="boolean" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
-        <param name="filter_exon" type="boolean" label="Filter out all single-exon genes"/>
+        <param argument="--ignore_tx_phase" type="boolean" truevalue="--ignore_tx_phase" falsevalue="" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/>
+        <param argument="--filter_single_exon_genes" type="boolean" truevalue="--filter_single_exon_genes" falsevalue="" label="Filter out all single-exon genes"/>
     </inputs>
 
     <outputs>
@@ -55,7 +51,6 @@
             <filter>score_tab</filter>
         </data>
     </outputs>
-
     <tests>
         <test expect_num_outputs="1">
             <param name="gtf_file" value="braker.gtf" ftype="gtf"/>
@@ -71,12 +66,11 @@
             <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/>
             <output name="output_tab" ftype="txt" file="output_tab.txt">
                 <assert_contents>
-                    <has_n_lines n="667"/>
+                    <has_n_lines n="668"/>
                 </assert_contents>
             </output>
         </test>
     </tests>
-
     <help><![CDATA[
         tsebra_  TSEBRA is a combinatorial tool that selects transcripts from genetic predictions based on support by extrinsic evidence 
         in the form of introns and start/stop codpns. This tool has been developed to combine BRAKER predictions.