diff chira_extract.xml @ 11:a618f28e1496 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 51f68a6d51d9e87f8e54021ce760b1506a3589b8"

--- a/chira_extract.xml	Sat Jun 06 08:12:25 2020 -0400
+++ b/chira_extract.xml	Sun Jun 14 17:37:05 2020 -0400
@@ -32,9 +32,12 @@
         #end if
         $hybridize
         $seed_interaction
+        -sbp '$seed_bp'
+        -smpu '$seed_min_pu'
+        -acc '$accessibility'
+        -accw '$acc_width'
+        -m '$intarna_mode'
         $summarize
-        -a '$accessibility'
-        -m '$intarna_mode'
         -p "\${GALAXY_SLOTS:-2}"
         -o ./
     ]]></command>
@@ -93,29 +96,39 @@
         <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
                label="Hybridize chimeric loci?"
                help="Turning this option on increases the run time of the tool significantly."/>
-        <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="false"
-               label="Enforce seed interaction?"/>
-        <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
-               label="Compute accessibility profiles for interacting sequences?"/>
         <param name="intarna_mode" type="select">
             <option value="H">Heuristic</option>
             <option value="M">Exact</option>
             <option value="S">Seed-only</option>
         </param>
+        <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="true"
+               label="Enforce seed interaction?"/>
+        <param name="seed_bp" type="integer" value="5" min="2" max="20"
+               label="Number of inter-molecular base pairs within the seed region"
+               help="IntaRNA --seedBP parameter"/>
+        <param name="seed_min_pu" type="float" value="0" min="0" max="1"
+               label="Minimal unpaired probability (per sequence) a seed region may have"
+               help="IntaRNA --seedMinPu parameter"/>
+        <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
+               label="Compute accessibility profiles for interacting sequences?"/>
+        <param name="acc_width" type="integer" value="150" min="0" max="99999"
+               label="Sliding window size for accessibility computation"
+               help="IntaRNA --accW parameter"/>
+        <param name="temperature" type="float" value="37" min="0" max="100"
+               label="IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters"/>
         <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
                label="Summarize interactions at loci level?"/>
     </inputs>
 
     <outputs>
         <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
-        <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/>
         <data format="tabular" name="interactions" from_work_dir="interactions" label="ChiRA interaction summary on ${on_string}">
             <filter>summarize == True</filter>
         </data>
     </outputs>
 
     <tests>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="2">
             <param name="loci" value="loci.counts"/>
             <param name="ref_type" value="split"/>
             <param name="ref_fasta1" value="ref1.fasta"/>
@@ -124,7 +137,6 @@
             <param name="hybridize" value="true" />
             <param name="summarize" value="true" />
             <output name="chimeras" file="chimeras"/>
-            <output name="singletons" file="singletons"/>
             <output name="interactions" file="interactions"/>
         </test>
     </tests>