diff bam2wig.xml @ 63:27e16a30667a draft default tip

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

--- a/bam2wig.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/bam2wig.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -1,19 +1,14 @@
 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>
-        converts all types of RNA-seq data from .bam to .wig
+        converts all types of RNA-seq data from BAM to Wiggle
     </description>
     <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[bam2wig.py --version]]></version_command>
-
     <command><![CDATA[
         @BAM_SAM_INPUTS@
         bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile
@@ -44,9 +39,9 @@
         ]]>
     </command>
     <inputs>
-        <expand macro="bam_param" />
+        <expand macro="bam_param"/>
         <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>
-        <expand macro="multihits_param" />
+        <expand macro="multihits_param"/>
         <conditional name="wigsum_type">
             <param name="wigsum_type_selector" type="select" label="Normalization">
                 <option value="normalize">Normalize to specified sum</option>
@@ -57,9 +52,8 @@
             </when>
             <when value="raw"/>
         </conditional>
-        <expand macro="strand_type_param" />
+        <expand macro="strand_type_param"/>
     </inputs>
-
     <outputs>
         <data format="wig" name="output" from_work_dir="outfile.wig">
             <filter>strand_type['strand_specific'] == 'none'</filter>
@@ -71,21 +65,20 @@
             <filter>strand_type['strand_specific'] != 'none'</filter>
         </data>
     </outputs>
-
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="chromsize" value="hg19.chrom.sizes"/>
             <output name="output" file="testwig.wig"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="chromsize" value="hg19.chrom.sizes"/>
             <param name="multihits_type_selector" value="skip_multihits"/>
             <param name="mapq" value="20"/>
             <output name="output" file="testwig.wig"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="chromsize" value="hg19.chrom.sizes"/>
             <param name="strand_specific" value="pair"/>
@@ -93,7 +86,7 @@
             <output name="outputfwd" file="testwig.Forward.wig"/>
             <output name="outputrv" file="testwig.Reverse.wig"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="chromsize" value="hg19.chrom.sizes"/>
             <param name="wigsum_type_selector" value="normalize"/>
@@ -101,7 +94,6 @@
             <output name="output" file="testwig_wigsum100.wig"/>
         </test>
     </tests>
-
     <help><![CDATA[
 bam2wig.py
 ++++++++++
@@ -149,7 +141,5 @@
 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>