diff FPKM_count.xml @ 63:27e16a30667a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de

--- a/FPKM_count.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/FPKM_count.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -3,15 +3,10 @@
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
-
     <expand macro="bio_tools"/>
-
-    <expand macro="requirements" />
-
-    <expand macro="stdio" />
-
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <version_command><![CDATA[FPKM_count.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}'
@@ -36,12 +31,11 @@
         --single-read="${singleread}"
         ]]>
     </command>
-
     <inputs>
-        <expand macro="bam_param" />
-        <expand macro="refgene_param" />
-        <expand macro="strand_type_param" />
-        <expand macro="multihits_param" />
+        <expand macro="bam_param"/>
+        <expand macro="refgene_param"/>
+        <expand macro="strand_type_param"/>
+        <expand macro="multihits_param"/>
         <param name="onlyexonic" type="boolean" value="false" truevalue="--only-exonic" falsevalue="" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" help="(--only-exonic)"/>
         <param name="singleread" type="select" label="How should read-pairs that only have one end mapped be counted?" help="(--single-read)">
             <option value="1" selected="true">Treat it as a whole fragment (1)</option>
@@ -49,18 +43,16 @@
             <option value="0">Ignore it (0)</option>
         </param>
     </inputs>
-
     <outputs>
         <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/>
     </outputs>
-
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <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="output" file="output01.tab"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <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">
@@ -69,11 +61,10 @@
             </conditional>
             <output name="output" file="output02.tab"/>
             <assert_command>
-                <has_text text="--mapq=20" />
+                <has_text text="--mapq=20"/>
             </assert_command>
         </test>
     </tests>
-
     <help><![CDATA[
 FPKM_count.py
 +++++++++++++
@@ -134,7 +125,5 @@
 
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>