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diff t_coffee.xml @ 9:e3507be607eb draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/t_coffee commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
author earlhaminst
date Mon, 24 Feb 2025 11:00:35 +0000
parents ae69d14b6fbf
children
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--- a/t_coffee.xml	Thu Jan 14 12:14:52 2021 +0000
+++ b/t_coffee.xml	Mon Feb 24 11:00:35 2025 +0000
@@ -87,7 +87,7 @@
             <option value="t_coffee_msa">t_coffee_msa</option>
             <option value="kalign_msa">kalign_msa</option>
         </param>
-        <param name="outputs" type="select" multiple="true" optional="false" display="checkboxes" label="Output formats">
+        <param name="outputs" type="select" multiple="true" optional="false" label="Output formats">
             <option value="clustalw_aln">clustalw_aln</option>
             <option value="dnd" selected="true">dnd</option>
             <option value="fasta_aln">fasta_aln</option>
@@ -156,15 +156,39 @@
             <param name="method01" value="sap_pair,mustang_pair,TMalign_pair" />
             <param name="method02" value="mafft_msa,clustalw_msa,dialigntx_msa,poa_msa,probcons_msa,muscle_msa,t_coffee_msa,kalign_msa" />
             <param name="outputs" value="clustalw_aln,dnd,fasta_aln,fasta_seq,msf_aln,phylip,pir_aln,pir_seq,score_ascii,score_html" />
-            <output name="clustalw_aln" file="output3.clustal" />
+            <output name="clustalw_aln">
+                <assert_contents>
+                    <has_size size="44953" delta="1000" />
+                </assert_contents>
+            </output>
             <output name="dnd" file="output3.nhx" />
-            <output name="fasta_aln" file="output3.fasta_aln" />
+            <output name="fasta_aln">
+                <assert_contents>
+                    <has_size size="21797" delta="500" />
+                </assert_contents>
+            </output>
             <output name="fasta_seq" file="output3.fasta_seq" />
-            <output name="msf_aln" file="output3.msf" />
-            <output name="phylip" file="output3.phylip" />
-            <output name="pir_aln" file="output3.pir_aln" />
+            <output name="msf_aln">
+                <assert_contents>
+                    <has_size size="41823" delta="1000" />
+                </assert_contents>
+            </output>
+            <output name="phylip">
+                <assert_contents>
+                    <has_size size="27310" delta="600" />
+                </assert_contents>
+            </output>
+            <output name="pir_aln">
+                <assert_contents>
+                    <has_size size="21827" delta="500" />
+                </assert_contents>
+            </output>
             <output name="pir_seq" file="output3.pir_seq" />
-            <output name="score_ascii" file="output3.txt" />
+            <output name="score_ascii">
+                <assert_contents>
+                    <has_size size="42613" delta="1000" />
+                </assert_contents>
+            </output>
             <output name="score_html">
                 <assert_contents>
                     <has_text text="ENSMUST00000091" />
@@ -183,7 +207,7 @@
 
 This wrapper offers selected advanced T-Coffee options like the selection of the alignment methods to use: ''Pairwise Structual Method'', ''Multiple Sequence Alignment Methods'' or ''Pairwise Sequence Alignment Methods''.
 
-The T-Coffee documentation can be found at http://www.tcoffee.org/Projects/tcoffee/ .
+The T-Coffee documentation can be found at https://tcoffee.org/Projects/tcoffee/index.html .
 
 **Example**