diff t_coffee.xml @ 8:ae69d14b6fbf draft default tip

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"

--- a/t_coffee.xml	Wed Sep 18 06:37:40 2019 -0400
+++ b/t_coffee.xml	Thu Jan 14 12:14:52 2021 +0000
@@ -1,7 +1,10 @@
-<tool id="t_coffee" name="T-Coffee" version="11.0.8_1">
+<tool id="t_coffee" name="T-Coffee" version="@TOOL_VERSION@">
     <description>multiple sequence alignment</description>
+    <macros>
+        <token name="@TOOL_VERSION@">13.45.0.4846264</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.8">t_coffee</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">t-coffee</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" />
@@ -60,28 +63,29 @@
                 <param name="input" type="data" format="fasta" label="FASTA sequences" />
             </when>
         </conditional>
-        <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Method">
-            <option value="sap_pair">sap_pair</option>
-            <option value="TMalign_pair">TMalign_pair</option>
-            <option value="mustang_pair">mustang_pair</option>
-        </param>
-        <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">
-            <option value="pcma_msa">pcma_msa</option>
-            <option value="clustalw_msa">clustalw_msa</option>
-            <option value="dialigntx_msa">dialigntx_msa</option>
-            <option value="poa_msa">poa_msa</option>
-            <option value="muscle_msa">muscle_msa</option>
-            <option value="probcons_msa">probcons_msa</option>
-            <option value="t_coffee_msa">t_coffee_msa</option>
-            <option value="amap_msa">amap_msa</option>
-            <option value="kalign_msa">kalign_msa</option>
-        </param>
         <param name="method03" type="select" display="checkboxes" multiple="true" label="Pairwise Sequence Alignment Methods">
             <option value="fast_pair">fast_pair</option>
             <option value="clustalw_pair">clustalw_pair</option>
             <option value="lalign_id_pair">lalign_id_pair</option>
             <option value="slow_pair">slow_pair</option>
             <option value="proba_pair">proba_pair</option>
+            <option value="t_coffee_pair">t_coffee_pair</option>
+        </param>
+        <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Alignment Methods">
+            <option value="sap_pair">sap_pair</option>
+            <option value="mustang_pair">mustang_pair</option>
+            <option value="TMalign_pair">TMalign_pair</option>
+        </param>
+        <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">
+            <option value="3dcoffee_msa">3dcoffee_msa</option>
+            <option value="mafft_msa">mafft_msa</option>
+            <option value="clustalw_msa">clustalw_msa</option>
+            <option value="dialigntx_msa">dialigntx_msa</option>
+            <option value="poa_msa">poa_msa</option>
+            <option value="probcons_msa">probcons_msa</option>
+            <option value="muscle_msa">muscle_msa</option>
+            <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">
             <option value="clustalw_aln">clustalw_aln</option>
@@ -97,7 +101,7 @@
         </param>
     </inputs>
     <outputs>
-        <data name="clustalw_aln" format="clustalw" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln">
+        <data name="clustalw_aln" format="clustal" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln">
             <filter>'clustalw_aln' in outputs</filter>
         </data>
         <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: newick.dnd" from_work_dir="t_coffee_out.dnd">
@@ -112,7 +116,7 @@
         <data name="msf_aln" format="msf" label="${tool.name} on ${on_string}: msf_aln" from_work_dir="t_coffee_out.msf_aln">
             <filter>'msf_aln' in outputs</filter>
         </data>
-        <data name="phylip" format="phyloxml" label="${tool.name} on ${on_string}: phylip" from_work_dir="t_coffee_out.phylip">
+        <data name="phylip" format="phylip" label="${tool.name} on ${on_string}: phylip" from_work_dir="t_coffee_out.phylip">
             <filter>'phylip' in outputs</filter>
         </data>
         <data name="pir_aln" format="pir" label="${tool.name} on ${on_string}: pir_aln" from_work_dir="t_coffee_out.pir_aln">
@@ -121,7 +125,7 @@
         <data name="pir_seq" format="pir" label="${tool.name} on ${on_string}: pir_seq" from_work_dir="t_coffee_out.pir_seq">
             <filter>'pir_seq' in outputs</filter>
         </data>
-        <data name="score_ascii" format="ascii" label="${tool.name} on ${on_string}: score_ascii" from_work_dir="t_coffee_out.score_ascii">
+        <data name="score_ascii" format="txt" label="${tool.name} on ${on_string}: score_ascii" from_work_dir="t_coffee_out.score_ascii">
             <filter>'score_ascii' in outputs</filter>
         </data>
         <data name="score_html" format="html" label="${tool.name} on ${on_string}: score_html" from_work_dir="t_coffee_out.score_html">
@@ -129,20 +133,47 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="filter_fasta" value="no" />
             <param name="input" value="input.fasta" ftype="fasta" />
             <param name="method02" value="clustalw_msa" />
             <param name="outputs" value="fasta_aln" />
-            <output name="fasta_aln" file="output1.fasta" ftype="fasta" />
+            <output name="fasta_aln" file="output1.fasta" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="filter_fasta" value="yes" />
             <param name="fasta_input" value="input.fasta" ftype="fasta" />
             <param name="identifiers" value="ids.txt" ftype="txt" />
             <param name="method02" value="clustalw_msa" />
             <param name="outputs" value="fasta_aln" />
-            <output name="fasta_aln" file="output2.fasta" ftype="fasta" />
+            <output name="fasta_aln" file="output2.fasta" />
+        </test>
+        <!-- Test all non-builtin methods and all outputs -->
+        <test expect_num_outputs="10">
+            <param name="filter_fasta" value="no" />
+            <param name="input" value="input.fasta" ftype="fasta" />
+            <param name="method03" value="clustalw_pair,t_coffee_pair" />
+            <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="dnd" file="output3.nhx" />
+            <output name="fasta_aln" file="output3.fasta_aln" />
+            <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="pir_seq" file="output3.pir_seq" />
+            <output name="score_ascii" file="output3.txt" />
+            <output name="score_html">
+                <assert_contents>
+                    <has_text text="ENSMUST00000091" />
+                    <has_text text="ENSCAFT00000026" />
+                    <has_text text="ENSMUST00000005" />
+                    <has_text text="ENSRNOT00000019" />
+                    <has_text text="ENSPTRT00000013" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[