Mercurial > repos > iuc > tetyper

changeset 3:2b21643ce8d7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
author iuc
date Sun, 15 Dec 2024 09:08:07 +0000
parents edcf603bedfd
children
files tetyper.xml
diffstat 1 files changed, 27 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/tetyper.xml	Tue Nov 16 19:57:38 2021 +0000
+++ b/tetyper.xml	Sun Dec 15 09:08:07 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy1">
+<tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy2" profile="23.1">
     <description>Transposable Element Typer</description>
     <macros>
         <token name="@TOOL_VERSION@">1.1</token>
@@ -105,12 +105,12 @@
         <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/>
         <data name="blast" format="tabular" from_work_dir="output_blast.txt" label="${tool.name} on ${on_string}: BLAST alignment"/>
         <data name="alignment" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: BWA alignment"/>
-        <data name="log" format="text" from_work_dir="output.log" label="${tool.name} on ${on_string}: log">
+        <data name="log" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: log">
             <filter>include_log</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <param name="reference" value="Tn4401b-1.fasta" />
             <conditional name="collection_paired">
                 <param name="selector" value="paired" />
@@ -119,7 +119,7 @@
             </conditional>
             <output name="summary" file="output_summary_1.txt" />
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="reference" value="Tn4401b-1.fasta" />
             <conditional name="collection_paired">
                 <param name="selector" value="paired" />
@@ -136,7 +136,7 @@
             </conditional>
             <output name="summary" file="output_summary_2.txt" />
         </test>
-        <test>
+        <test expect_num_outputs="5">
             <param name="reference" value="Tn4401b-1.fasta" />
             <conditional name="collection_paired">
                 <param name="selector" value="paired" />
@@ -151,7 +151,29 @@
                 <param name="struct_profiles_source_selector" value="tool_data_table" />
                 <param name="struct_profiles" value="Tn4401b_struct_profiles" />
             </conditional>
+            <param name="include_log" value="true"/>
             <output name="summary" file="output_summary_2.txt" />
+            <output name="snps">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+            <output name="blast">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="12"/>
+                </assert_contents>
+            </output>
+            <output name="alignment">
+                <assert_contents>
+                    <has_size min="1"/>
+                </assert_contents>
+            </output>
+            <output name="log">
+                <assert_contents>
+                    <has_text text="Final output written to: output_summary.txt"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>