Mercurial > repos > iuc > jellyfish

diff jellyfish.xml @ 1:11658afb8c87 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit 173be51ac6f23888ad4065877762b67e4cc9ed6e
author iuc
date Wed, 01 Nov 2023 09:32:45 +0000
parents b4038a4d48f5
children dcd30574a456
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line diff
--- a/jellyfish.xml	Mon Apr 12 18:18:53 2021 +0000
+++ b/jellyfish.xml	Wed Nov 01 09:32:45 2023 +0000
@@ -3,6 +3,9 @@
         <token name="@WRAPPER_VERSION@">2.3.0</token>
         <token name="@VERSION_SUFFIX@">galaxy0</token>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">Jellyfish</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@WRAPPER_VERSION@">kmer-jellyfish</requirement>
     </requirements>
@@ -210,12 +213,17 @@
                 <param name="lower" value="1"/>
                 <param name="upper" value="20"/>
             </conditional>
-            <output name="jellyfish_db_txt" file="out.jf.txt" lines_diff="2"/>
+            <output name="jellyfish_db_txt">
+                <assert_contents>
+                    <has_line line="GTGATCGAGAGCCACAGCGTTA 1"/>
+                    <has_line line="GCCTAGTCGGGATCGTCACCTA 1"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <conditional name="commands">
                 <param name="command" value="histo"/>
-                <param name="input" value="out.jf"/>
+                <param name="input" value="out.jf" ftype="jellyfish"/>
                 <param name="low" value="1"/>
                 <param name="high" value="10000"/>
                 <param name="full" value="--full"/> 
@@ -226,7 +234,7 @@
         <test expect_num_outputs="1">
             <conditional name="commands">
                 <param name="command" value="dump"/>
-                <param name="input" value="out.jf"/>
+                <param name="input" value="out.jf" ftype="jellyfish"/>
                 <param name="lower_count" value="3"/>
             </conditional>
             <output name="jellyfish_fasta" ftype="fasta" file="dump.fasta"/>
@@ -234,14 +242,19 @@
         <test expect_num_outputs="1">
             <conditional name="commands">
                 <param name="command" value="dump"/>
-                <param name="input" value="out.jf"/>
+                <param name="input" value="out.jf" ftype="jellyfish"/>
                 <conditional name="format">
                     <param name="format_select" value="column"/>
                     <param name="tab" value="--tab"/>
                 </conditional>
                 <param name="upper_count" value="100"/>
             </conditional>
-            <output name="jellyfish_tsv" ftype="tsv" file="dump.tsv"/>
+            <output name="jellyfish_tsv" ftype="tsv">
+                <assert_contents>
+                    <has_line line="GTGATCGAGAGCCACAGCGTTA&#9;1"/>
+                    <has_line line="GCCTAGTCGGGATCGTCACCTA&#9;1"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[