Repository 'intarna'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/intarna

Changeset 16:f5d850723e63 (2024-09-18)
Previous changeset 15:0377acb3f91b (2024-01-25)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
modified:
intarna.xml
b
diff -r 0377acb3f91b -r f5d850723e63 intarna.xml
--- a/intarna.xml Thu Jan 25 13:12:23 2024 +0000
+++ b/intarna.xml Wed Sep 18 19:42:08 2024 +0000
[
b'@@ -1,74 +1,74 @@\n-<tool id="intarna" name="IntaRNA" version="3.4.0">\n+<tool id="intarna" name="IntaRNA" version="3.4.1" profile="23.0">\n     <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>\n     <macros>\n         <macro name="query_macro">\n-            <param argument="--query" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" />\n+            <param argument="--query" type="data" format="fasta" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format"/>\n             <conditional name="qAcc_cond">\n-                <param argument="--qAcc" help="" label="Accessibility computation" type="select">\n+                <param argument="--qAcc" type="select" label="Accessibility computation" help="">\n                     <option value="N">No accessibility contributions (\'N\')</option>\n                     <option selected="true" value="C">Computation of accessibilities (\'C\')</option>\n                     <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>\n                     <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>\n                 </param>\n-                <when value="N" />\n-                <when value="C" />\n+                <when value="N"/>\n+                <when value="C"/>\n                 <when value="P">\n-                    <param argument="--qAccFile" format="txt" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA" label="RNAplfold unpaired probability data" type="data" />\n+                    <param argument="--qAccFile" type="data" format="txt" label="RNAplfold unpaired probability data" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA"/>\n                 </when>\n                 <when value="E">\n-                    <param argument="--qAccFile" format="txt" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA" label="IntaRNA accessibility energy penalties (ED terms)" type="data" />\n+                    <param argument="--qAccFile" type="data" format="txt" label="IntaRNA accessibility energy penalties (ED terms)" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA"/>\n                 </when>\n             </conditional>\n-            <param argument="--qAccW" help="... for query accessibility computation. Set to 0 to use full sequence length" label="Max. interaction length" max="99999" min="0" type="integer" value="150" />\n-            <param argument="--qAccL" help="... for query accessibility computation. 0 defaults to sliding window size \'qAccW\'" label="Max. loop length" max="99999" min="0" type="integer" value="100" />\n+            <param argument="--qAccW" type="integer" min="0" max="99999" value="150" label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>\n+            <param argument="--qAccL" type="integer" min="0" max="99999" value="100" label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size \'qAccW"/>\n         </macro>\n         <macro name="target_macro">\n-            <param argument="--target" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Target sequence(s)" name="target" type="data" />\n+            <param argument="--target" type="data" format="fasta" label="Target sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format"/>\n             <conditional name="tAcc_cond">\n-                <param argument="--tAcc" help="" label="Accessibility computation" type="select">\n+                <param argument="--tAcc" type="select" '..b'cc.*)\\.led" visible="true"/>\n         </collection>\n         <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list">\n             <filter>\n@@ -352,7 +352,7 @@\n                 \'tAcc\' in advancedOptions[\'output\'][\'add_output_cond\'][\'add_output\']\n                 ))\n             </filter>\n-            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\\.led" visible="true" />\n+            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\\.led" visible="true"/>\n         </collection>\n         <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list">\n             <filter>\n@@ -362,7 +362,7 @@\n                 \'qPu\' in advancedOptions[\'output\'][\'add_output_cond\'][\'add_output\']\n                 ))\n             </filter>\n-            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\\.lpu" visible="true" />\n+            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\\.lpu" visible="true"/>\n         </collection>\n         <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list">\n             <filter>\n@@ -372,39 +372,39 @@\n                 \'tPu\' in advancedOptions[\'output\'][\'add_output_cond\'][\'add_output\']\n                 ))\n             </filter>\n-            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\\.lpu" visible="true" />\n+            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\\.lpu" visible="true"/>\n         </collection>\n     </outputs>\n     <tests>\n-        <test>\n+        <test expect_num_outputs="1">\n             <conditional name="advancedOptions">\n-                <param name="advancedSelector" value="basic" />\n+                <param name="advancedSelector" value="basic"/>\n                 <section name="query">\n-                    <param name="query" value="intarna_query.fa" />\n+                    <param name="query" value="intarna_query.fa"/>\n                 </section>\n                 <section name="target">\n-                    <param name="target" value="intarna_target.fa" />\n+                    <param name="target" value="intarna_target.fa"/>\n                 </section>\n             </conditional>\n-            <output file="intarna_result.tabular" name="outfile" />\n+            <output file="intarna_result.tabular" name="outfile"/>\n         </test>\n-        <test>\n+        <test expect_num_outputs="5">\n             <conditional name="advancedOptions">\n-                <param name="advancedSelector" value="advanced" />\n+                <param name="advancedSelector" value="advanced"/>\n                 <section name="query">\n-                    <param name="query" value="intarna_query.fa" />\n+                    <param name="query" value="intarna_query.fa"/>\n                 </section>\n                 <section name="target">\n-                    <param name="target" value="intarna_target.fa" />\n+                    <param name="target" value="intarna_target.fa"/>\n                 </section>\n                 <section name="output">\n                     <conditional name="add_output_cond">\n-                        <param name="selector" value="add" />\n-                        <param name="add_output" value="spotProb,qMinE,tAcc,qPu" />\n+                        <param name="selector" value="add"/>\n+                        <param name="add_output" value="spotProb,qMinE,tAcc,qPu"/>\n                     </conditional>\n                 </section>\n             </conditional>\n-            <output file="intarna_result.tabular" name="outfile" />\n+            <output file="intarna_result.tabular" name="outfile"/>\n             <output_collection count="4" name="spotProb_output" type="list">\n             </output_collection>\n             <output_collection count="4" name="qMinE_output" type="list">\n'