diff hyphy_cfel.xml @ 2:fb833dd994f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"

--- a/hyphy_cfel.xml	Tue Apr 20 19:50:17 2021 +0000
+++ b/hyphy_cfel.xml	Tue Apr 27 18:02:15 2021 +0000
@@ -1,37 +1,36 @@
 <?xml version="1.0"?>
-<tool id="hyphy_cfel" name="HyPhy-CFEL" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_cfel" name="HyPhy-CFEL" version="@VERSION@+galaxy1" profile="19.09">
     <description>Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$input_file' cfel_input.fa &&
-        ln -s '$input_nhx' cfel_input.nhx &&
+        @SYMLINK_FILES@
         hyphy contrast-fel
             --code '$gencodeid'
-            #for branch in str($branch_set).split(','):
-                --branch-set '$branch'
+            #for $i, $branch in enumerate($branch_repeat):
+                --branch-set '$branch.branch_label'
             #end for
             --srv '$srv'
             --permutations '$permutations'
             --pvalue '$pvalue'
             --qvalue '$qvalue'
             --output '$cfel_output'
-            cfel_input.fa
-            cfel_input.nhx
-            > '$cfel_log'
+            $input_file
+            @INPUT_TREE@
         @ERRORS@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
         <expand macro="gencode"/>
-        <param argument="--branch-set" type="select" multiple="true" min="2" max="2" label="Set of branches to test">
-            <option value="Internal branches">Internal branches</option>
-            <option value="Terminal branches">Terminal branches</option>
-            <option value="Random set of branches">Random set of branches</option>
-            <option value="Unlabeled branches">Unlabeled branches</option>
-        </param>
+        <repeat name="branch_repeat" title="Branch set" min="2">
+            <param name="branch_label" type="text" value="Test" optional="false" label="Label for set">
+                <sanitizer invalid_char="">
+                    <valid initial="default" />
+                </sanitizer>
+            </param>
+        </repeat>
         <param argument="--permutations" type="boolean" truevalue="Yes" falsevalue="No" label="Perform permutation significance tests"/>
         <param argument="--pvalue" type="float" value=".05" min="0" max="1" label="Significance value for site-tests"/>
         <param argument="--qvalue" type="float" value=".2" min="0" max="1" label="Significance value for FDR reporting"/>
@@ -41,14 +40,18 @@
         </param>
     </inputs>
     <outputs>
-        <data name="cfel_log" format="txt"/>
         <data name="cfel_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>
             <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
             <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
-            <param name="branch_set" value="Internal branches,Terminal branches" />
+            <repeat name="branch_repeat">
+                <param name="branch_label" value="Internal branches" />
+            </repeat>
+            <repeat name="branch_repeat">
+                <param name="branch_label" value="Terminal branches" />
+            </repeat>
             <output name="cfel_output" file="cfel-out1.json" compare="sim_size"/>
         </test>
     </tests>