--- a/kissplice.xml	Thu May 06 12:44:17 2021 +0000
+++ b/kissplice.xml	Sat Oct 05 19:54:14 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="kissplice" name="KisSplice" version="2.4.0+galaxy0" profile="@PROFILE@">
+<tool id="kissplice" name="KisSplice" version="2.4.0+galaxy1" profile="@PROFILE@">
     <description>is a local transcriptome assembler for SNPs, indels and AS events</description>
     <macros>
         <import>macros.xml</import>
@@ -26,7 +26,7 @@
         <param argument="-k" type="integer" value="41" label="K-mer length" />
         <param argument="-c" type="integer" value="2" label="K-mers present strictly less than this number of times in the dataset will be discarded (integer value required)" />
         <param argument="-C" type="float" value="0.05" label="Edges with relative coverage below this number are removed (value in [0,1) required)" />
-        <param name="output_context" argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" />
+        <param argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" />
         <param argument="--counts" type="select" label="Selecting how the counts will be reported">
             <option value="0">Total counts</option>
             <option value="1">Counts on junctions</option>
@@ -38,30 +38,61 @@
         </param>
     </inputs>
     <outputs>
-        <data name="type0a" format="fasta" label="Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa">
+        <data name="type0a" format="fasta" label="${tool.name} on ${on_string}: Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
-        <data name="type0b" format="fasta" label="Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa">
+        <data name="type0b" format="fasta" label="${tool.name} on ${on_string}: Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
-        <data name="type1" format="fasta" label="Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/>
-        <data name="type2" format="fasta" label="Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa">
+        <data name="type1" format="fasta" label="${tool.name} on ${on_string}: Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/>
+        <data name="type2" format="fasta" label="${tool.name} on ${on_string}: Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
-        <data name="type3" format="fasta" label="Short indels" from_work_dir="results/*_coherents_type_3.fa">
+        <data name="type3" format="fasta" label="${tool.name} on ${on_string}: Short indels" from_work_dir="results/*_coherents_type_3.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
-        <data name="type4" format="fasta" label="Other events" from_work_dir="results/*_coherents_type_4.fa">
+        <data name="type4" format="fasta" label="${tool.name} on ${on_string}: Other events" from_work_dir="results/*_coherents_type_4.fa">
             <filter>output_option == 'all_files'</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
             <param name="k" value="25"/>
             <param name="output_option" value="alternative_file" />
             <output name="type1" file="kissplice/alternative_splicing.fa"/>
         </test>
+        <test expect_num_outputs="6">
+            <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
+            <param name="k" value="25"/>
+            <param name="output_option" value="all_files" />
+            <output name="type0a">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="type0b">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="type1" file="kissplice/alternative_splicing.fa"/>
+            <output name="type2">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="type3">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <output name="type4">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 
@@ -82,17 +113,7 @@
 
     ]]></help>
     <expand macro="citations">
-        <citation type="bibtex">
-         @article{PMID:22537044,
-          author       = {Sacomoto, G. A. and Kielbassa, J. and Chikhi, R. and Uricaru, R. and Antoniou, P. and Sagot, M. F. and Peterlongo, P. and Lacroix, V.},
-          title        = {KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.},
-          journal      = {BMC Bioinformatics},
-          year         = {2012},
-          volume       = {13 Suppl 6},
-          pages        = {S5},
-          url          = {http://www.ncbi.nlm.nih.gov/pubmed/22537044},
-        }
-        </citation>
+        <citation type="doi">10.1186/1471-2105-13-S6-S5</citation>
     </expand>
 
 </tool>