diff FPKM_count.xml @ 62:473382134e56 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec

--- a/FPKM_count.xml	Sat Dec 10 11:23:05 2022 +0000
+++ b/FPKM_count.xml	Wed Feb 22 15:06:01 2023 +0000
@@ -15,7 +15,6 @@
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}'
-
         #if str($strand_type.strand_specific) == "pair"
             -d
             #if str($strand_type.pair_type) == "sd"
@@ -24,7 +23,6 @@
                 '1+-,1-+,2++,2--'
             #end if
         #end if
-
         #if str($strand_type.strand_specific) == "single"
             -d
             #if str($strand_type.single_type) == "s"
@@ -33,9 +31,7 @@
                 '+-,-+'
             #end if
         #end if
-
         @MULTIHITS@
-
         $onlyexonic
         --single-read="${singleread}"
         ]]>
@@ -55,14 +51,26 @@
     </inputs>
 
     <outputs>
-        <data format="xls" name="outputxls" from_work_dir="output.FPKM.xls"/>
+        <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/>
     </outputs>
 
     <tests>
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
-            <output name="outputxls" file="output.FPKM.xls"/>
+            <output name="output" file="output01.tab"/>
+        </test>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
+            <conditional name="multihits_type">
+                <param name="multihits_type_selector" value="skip_multihits"/>
+                <param name="mapq" value="20"/>
+            </conditional>
+            <output name="output" file="output02.tab"/>
+            <assert_command>
+                <has_text text="--mapq=20" />
+            </assert_command>
         </test>
     </tests>