diff hicHyperoptDetectLoops.xml @ 2:7f7c6ead2d0d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

--- a/hicHyperoptDetectLoops.xml	Thu Jan 12 17:22:44 2023 +0000
+++ b/hicHyperoptDetectLoops.xml	Wed Oct 18 10:36:42 2023 +0000
@@ -26,7 +26,10 @@
             #if '$runs':
                 --runs '$runs'
             #end if
-
+            
+            #if not $prefixLoop_selector == 'keep':
+                 --chrPrefixLoops $prefixLoop_selector
+            #end if
             --outputFileName hyperopt_result.txt
 
             --threads @THREADS@
@@ -34,13 +37,18 @@
     </command>
     <inputs>
         <expand macro="matrix_h5_cooler_macro" />
-        <param argument="--proteinFile" type='data' format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." />
-        <param argument="--maximumNumberOfLoops" type="integer" min='0' max='100000' label="Maximum number of loops" help= "The maximum number of loops that should be used for optimization computation." value='10000' />
-        <param argument="--resolution" type="integer" min='0' max='100000000' label="Resolution of the matrix" help="The matrix resolution of the Hi-C interaction matrix." value='10000' />
-        <param argument="--runs" type="integer" min='2' max='10000' label="Hyperopt runs" help= "The number of iterations hyperopt uses to search for a result" value='100' />
+        <param argument="--proteinFile" type="data" format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." />
+        <param argument="--maximumNumberOfLoops" type="integer" min="0" max="100000" label="Maximum number of loops" help= "The maximum number of loops that should be used for optimization computation." value="10000" />
+        <param argument="--resolution" type="integer" min="0" max="100000000" label="Resolution of the matrix" help="The matrix resolution of the Hi-C interaction matrix." value="10000" />
+        <param name="prefixLoop_selector" type="select" label="Add, remove, or keep the chr-prefix of the loop/TAD data">
+            <option value="keep" selected="True">Keep</option>
+            <option value="add">Add</option>
+            <option value="remove">Remove</option>
+        </param>
+        <param argument="--runs" type="integer" min="2" max="10000" label="Hyperopt runs" help= "The number of iterations hyperopt uses to search for a result" value="100" />
     </inputs>
     <outputs>
-        <data name='hyperopt_result' from_work_dir='hyperopt_result.txt' format='txt' label='Computed parameters for hicDetectLoops' />
+        <data name="hyperopt_result" from_work_dir="hyperopt_result.txt" format="txt" label="Computed parameters for hicDetectLoops" />
     </outputs>
     <tests>
         <test>