Mercurial > repos > nilesh > rseqc

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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
line wrap: on
line diff
--- a/read_hexamer.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/read_hexamer.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -6,12 +6,9 @@
         <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[read_hexamer.py --version]]></version_command>
-
     <command><![CDATA[
         #import re
         #set $input_list = []
@@ -39,51 +36,48 @@
         > '${output}'
         ]]>
     </command>
-
     <inputs>
-        <param name="inputs" type="data" label="Read sequences in fasta or fastq format" format="fasta,fastq,fastqsanger,fastq.gz,fastqsanger.gz" help="(--input)" multiple="true" />
-        <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)" />
-        <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)" />
+        <param name="inputs" type="data" label="Read sequences in fasta or fastq format" format="fasta,fastq,fastqsanger,fastq.gz,fastqsanger.gz" help="(--input)" multiple="true"/>
+        <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)"/>
+        <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)"/>
     </inputs>
-
     <outputs>
-        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
     </outputs>
-
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
             <output name="output">
                 <assert_contents>
-                    <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq" />
-                    <has_text text="0.002173913043478261" />
+                    <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq"/>
+                    <has_text text="0.002173913043478261"/>
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/>
             <output name="output">
                 <assert_contents>
-                    <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz" />
-                    <has_text text="0.002173913043478261" />
+                    <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz"/>
+                    <has_text text="0.002173913043478261"/>
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq"/>
             <output name="output">
                 <assert_contents>
-                    <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq" />
-                    <has_text text="0.002173913043478261" />
+                    <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq"/>
+                    <has_text text="0.002173913043478261"/>
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
             <output name="output">
                 <assert_contents>
-                    <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1" />
-                    <has_text text="0.002173913043478261" />
+                    <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1"/>
+                    <has_text text="0.002173913043478261"/>
                 </assert_contents>
             </output>
         </test>
@@ -99,7 +93,6 @@
         </test>
         -->
     </tests>
-
     <help><![CDATA[
 read_hexamer.py
 +++++++++++++++++++++
@@ -130,7 +123,5 @@
 
 ]]>
     </help>
-
-    <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>