diff spatyper.xml @ 2:0d2243ed7833 draft default tip

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit f3fb3601f726fd8f18dc42e6a83a9f92a7f27712

--- a/spatyper.xml	Mon Mar 20 20:52:30 2023 +0000
+++ b/spatyper.xml	Tue Apr 18 23:06:33 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="spatyper" name="Generate spa type identification" version="@VERSION@+galaxy0" profile="20.01">
+<tool id="spatyper" name="Generate spa type identification" version="@VERSION@+galaxy1" profile="20.01">
     <macros>
         <token name="@VERSION@">0.3.3</token>
     </macros>
@@ -6,24 +6,18 @@
         <requirement type="package" version="@VERSION@">spatyper</requirement>
     </requirements>
     <command detect_errors="aggressive"> <![CDATA[
-        spaTyper -f '${input1}' -r '${input2}' > '${output1}' 
+        spaTyper -f '${input}' --output '${output}' 
     ]]> </command>
     <inputs>
-        <param type="data" name="input1" format="fasta" label="SPA Fasta file" help="Staphylococcus aureus - staphylococcal protein A fasta file. This will be assigned a type based on its repeat region."/>
-        <param type="data" name="input2" format="fasta" label="Repeats Library Multifasta" help="A multifasta representing a set of known repeat regions found in staphylococcal protein A. This can be downloaded at (http://spa.ridom.de/dynamic/sparepeats.fasta)"/>
+        <param type="data" name="input" format="fasta" label="SPA Fasta file" help="Staphylococcus aureus - staphylococcal protein A fasta file. This will be assigned a type based on its repeat region."/>
     </inputs>
     <outputs>
-        <data name="output1" format="txt" />
+        <data name="output" format="tsv"/>
     </outputs>
     <tests>
         <test>
-            <param name="input1" value="input.fasta"/>
-            <param name="input2" value="sparepeats.fasta"/>
-            <output name="output1">
-                <assert_contents>
-                    <has_text text = "t11215" />
-                </assert_contents>
-            </output>
+            <param name="input" value="input.fasta"/>
+            <output name="output" file="output.tsv" ftype="tsv"/>
         </test>
     </tests>
     <help><![CDATA[