diff locarna_multiple.xml @ 3:7554c0df9139 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042

--- a/locarna_multiple.xml	Sat Jan 21 17:38:28 2017 -0500
+++ b/locarna_multiple.xml	Mon Dec 05 14:28:49 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@VERSION@.1">
+<tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>
         Multiple Alignment and Folding of RNAs (mlocarna)
     </description>
@@ -22,7 +22,8 @@
     #end if
 
     --tgtdir mlocarna_results
-    --width 60
+    ## maybe reenable later? see  https://github.com/s-will/LocARNA/issues/77
+    ## --width 60
     
     ## -------------------- alignment mode and specific options
     #
@@ -65,10 +66,9 @@
 
     @STDOUT_ARGS@
 
-    #if 'clustal_strict' in str($outputs).split(",")
+    #if 'strict' in str($outputs).split(",")
         && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
     #end if
-
     ]]></command>
 
     <inputs>
@@ -93,8 +93,7 @@
                    help="Note that local alignment mode usually requires to turn off 
                          the 'max-diff' heuristic (maximal difference for alignment traces)."
                    >
-                <option value="global_locarna">Global alignment
-                (LocARNA)</option>
+                <option value="global_locarna">Global alignment (LocARNA)</option>
                 <option value="local_locarna">Local alignment (LocARNA)</option>
                 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
                 <option value="sparse">Global fast alignment (SPARSE)</option>
@@ -129,46 +128,33 @@
                     <expand macro="common_heuristic_parameters_sparse" />
                 </section>
             </when>
-
         </conditional>
-        
-        <param name="outputs" type="select" display="checkboxes" multiple="True" 
+        <param name="outputs" type="select" display="checkboxes" multiple="true" 
                label="Output options">
-            <option value="clustal_strict" selected="True">Output alignment
-            in ClustalW format</option>
-            <option value="clustal" selected="False">Output alignment
-            in constraint-annotated ClustalW format</option>
-            <option value="stockholm" selected="False">Output
-            alignment in Stockholm format</option>
-            <option value="pp" selected="False">Output
-            alignment in LocARNA's PP 2.0 format</option>
-            <option value="mlocarna_results" selected="False">
-            Output LocARNA results archive (tar.gz)</option>
+            <option value="strict" selected="true">Alignment in ClustalW format</option>
+            <option value="clustal" selected="false">Alignment in constraint-annotated ClustalW format</option>
+            <option value="stockholm" selected="false">Alignment in Stockholm format</option>
+            <option value="pp" selected="false">Alignment in LocARNA's PP 2.0 format</option>
+            <option value="mlocarna_results" selected="false">LocARNA results archive (tar.gz)</option>
         </param>
-        
         <param name="stdout_verbosity" type="select" label="Standard output verbosity">
-            <option value="--quiet">Don't report standard
-            output</option>
+            <option value="--quiet">Don't report standard output</option>
             <option value="">Non verbose</option>
             <option value="--verbose">Verbose</option>
             <option value="--moreverbose">More verbose</option>
         </param>
-               
         <section name="Scoring" title="Scoring parameters">
             <expand macro="common_scoring_parameters" />
         </section>
-        
         <section name="Folding" title="RNA folding parameters">
             <expand macro="plfolding_parameters" />
             <expand macro="common_folding_parameters" />
             <expand macro="alifold_consensus_parameter" />
         </section>
-
         <section name="Heuristics" title="Heuristic parameters">
             <expand macro="common_heuristic_parameters" />
             <expand macro="max_diff_parameters_aln" />
         </section>
-
         <section name="Constraints" title="Constraint parameters">
             <expand macro="bed_anchors" />
             <expand macro="common_constraint_parameters" />
@@ -180,33 +166,59 @@
     </outputs>
     
     <tests>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_data" value="archaea.fa" />
             <param name="stdout_verbosity" value="" />
             <param name="max_diff_mode_selector" value="max-diff" />
             <param name="max_diff" value="20" />
-            <output name="stdout" file="archaea-default.stdout" />
+            <param name="outputs" value="clustal,strict"/>
+            <output name="stdout" file="archaea-default.stdout" lines_diff="2" />
+            <output name="clustal">
+                <assert_contents>
+                    <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
+            <output name="clustal_strict">
+                <assert_contents>
+                    <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_data" value="haca.snoRNA.fa" />
             <param name="stdout_verbosity" value="" />
-            <output name="stdout" file="haca.snoRNA-default.stdout" />
+            <output name="stdout" file="haca.snoRNA-default.stdout" lines_diff="2" />
+            <output name="clustal_strict">
+                <assert_contents>
+                    <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_data" value="archaea.fa" />
             <param name="stdout_verbosity" value="" />
             <param name="outputs" value="clustal" />
             <param name="alignment_mode_selector" value="probabilistic" />
-            <output name="clustal" file="archaea-probabilistic.aln" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
+            <output name="clustal" file="archaea-probabilistic.aln" lines_diff="2"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_data" value="archaea.fa" />
             <param name="stdout_verbosity" value="" />
             <param name="outputs" value="clustal" />
             <param name="max_diff_mode_selector" value="max-diff-aln" />
             <param name="max_diff_aln" value="archaea-ref.aln" />
             <param name="max_diff" value="2" />
-            <output name="clustal" file="archaea-ref_result.aln" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
+            <output name="clustal" file="archaea-ref_result.aln" lines_diff="2"/>
         </test>
     </tests>