# HG changeset patch
# User iuc
# Date 1638006934 0
# Node ID f9cb3a4339c29112b9d8efa2f3cf506b8e9e439d
# Parent  b2b8e75a962ddabd8d0aed76a02d0655fa86cf69
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"

diff -r b2b8e75a962d -r f9cb3a4339c2 codeml.xml
--- a/codeml.xml	Wed Sep 16 16:46:06 2020 +0000
+++ b/codeml.xml	Sat Nov 27 09:55:34 2021 +0000
@@ -1,4 +1,4 @@
-<tool name="codeML" id="codeml" version="@WRAPPER_VERSION@+galaxy1" profile="18.01">
+<tool name="codeML" id="codeml" version="@TOOL_VERSION@+galaxy2" profile="18.01">
     <description>
         Detects positive selection (paml package)
     </description>
@@ -8,7 +8,7 @@
     </macros>
 
     <requirements>
-        <requirement type="package" version="@WRAPPER_VERSION@">paml</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">paml</requirement>
     </requirements>
 
     <version_command><![CDATA[ codeml /dev/null 2>&1 | tail -1 ]]></version_command>
@@ -56,7 +56,7 @@
         ncatG = $adv.ncatG  * # of categories in dG of NSsites models
       fix_rho = $adv.fix_rho  * 0: estimate rho; 1: fix it at rho
           rho = $adv.rho * initial or fixed rho,   0:no correlation
-        getSE = $adv.getSE  * 0: don't want them, 1: want S.E.s of estimates
+        getSE = $adv.getSE  * 0: dont want them, 1: want S.E.s of estimates
  RateAncestor = $adv.RateAncestor  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
    Small_Diff = $adv.Small_Diff
     cleandata = $adv.cleandata  * remove sites with ambiguity data (1:yes, 0:no)?
@@ -238,13 +238,13 @@
 
     <outputs>
         <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" />
-        <data format="txt" name="2ngdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
+        <data format="txt" name="twongdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
             <filter>adv['seqtype']=="1"</filter>
         </data>
-        <data format="txt" name="2ngds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
+        <data format="txt" name="twongds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
             <filter>adv['seqtype']=="1"</filter>
         </data>
-        <data format="txt" name="2ngt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
+        <data format="txt" name="twongt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
             <filter>adv['seqtype']=="1"</filter>
         </data>
         <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/>
@@ -252,25 +252,25 @@
         <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/>
         <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/>
         <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/>
-        <data format="txt" name="4fold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
+        <data format="txt" name="fourfold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
             <filter>adv['verbose']=="1"</filter>
         </data>
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="9">
             <conditional name="compat_model" >
                 <param name="brmodel" value="0" />
                 <param name="NSsites" value="0" />
             </conditional>
-            <param name="adv.fix_omega" value="0" />
-            <param name="adv.omega" value="0.2" />
+            <param name="adv|fix_omega" value="0" />
+            <param name="adv|omega" value="0.2" />
             <param name="RateAncestor" value="1" />
             <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
-            <param name="tree" ftype="txt" value="RAxML_bestTree" />
-            <output name="2ngdn" value="1_2ngdn" />
-            <output name="2ngds" value="1_2ngds" />
-            <output name="2ngt" value="1_2ngt" />
+            <param name="tree" value="RAxML_bestTree" ftype="nhx" />
+            <output name="twongdn" value="1_2ngdn" />
+            <output name="twongds" value="1_2ngds" />
+            <output name="twongt" value="1_2ngt" />
             <output name="run">
                 <assert_contents>
                     <has_text text="CODONML (in paml version 4.9, March 2015)"/>
@@ -279,19 +279,19 @@
             </output>
             <output name="ctl" value="1_codeml.ctl" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="9">
             <conditional name="compat_model" >
                 <param name="brmodel" value="2" />
                 <param name="NSsites" value="0" />
             </conditional>
-            <param name="adv.fix_omega" value="0" />
-            <param name="adv.omega" value="0.2" />
+            <param name="adv|fix_omega" value="0" />
+            <param name="adv|omega" value="0.2" />
             <param name="RateAncestor" value="1" />
             <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
-            <param name="tree" ftype="txt" value="tree_model2" />
-            <output name="2ngdn" value="2_2ngdn" />
-            <output name="2ngds" value="2_2ngds" />
-            <output name="2ngt" value="2_2ngt" />
+            <param name="tree" value="tree_model2" ftype="nhx" />
+            <output name="twongdn" value="2_2ngdn" />
+            <output name="twongds" value="2_2ngds" />
+            <output name="twongt" value="2_2ngt" />
             <output name="run">
                 <assert_contents>
                     <has_text text="CODONML (in paml version 4.9, March 2015)"/>
@@ -300,19 +300,19 @@
             </output>
             <output name="ctl" value="2_codeml.ctl" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="9">
             <conditional name="compat_model" >
                 <param name="brmodel" value="3" />
                 <param name="NSsites" value="2" />
             </conditional>
-            <param name="adv.fix_omega" value="0" />
-            <param name="adv.omega" value="0.2" />
+            <param name="adv|fix_omega" value="0" />
+            <param name="adv|omega" value="0.2" />
             <param name="RateAncestor" value="1" />
             <param name="concat_nuc" ftype="fasta" value="concat.fasta" />
-            <param name="tree" ftype="txt" value="tree_model3" />
-            <output name="2ngdn" value="3_2ngdn" />
-            <output name="2ngds" value="3_2ngds" />
-            <output name="2ngt" value="3_2ngt" />
+            <param name="tree" value="tree_model3" ftype="nhx" />
+            <output name="twongdn" value="3_2ngdn" />
+            <output name="twongds" value="3_2ngds" />
+            <output name="twongt" value="3_2ngt" />
             <output name="run">
                 <assert_contents>
                     <has_text text="CODONML (in paml version 4.9, March 2015)"/>
diff -r b2b8e75a962d -r f9cb3a4339c2 macros.xml
--- a/macros.xml	Wed Sep 16 16:46:06 2020 +0000
+++ b/macros.xml	Sat Nov 27 09:55:34 2021 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">4.9</token>
+    <token name="@TOOL_VERSION@">4.9</token>
     <xml name="FSsites_br0" >
         <param argument="NSsites" type="select" label="Site model ; fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0" >
             <option value="0" selected="true">0 : e.g. basic model if model=0</option>
diff -r b2b8e75a962d -r f9cb3a4339c2 test-data/1_codeml.ctl
--- a/test-data/1_codeml.ctl	Wed Sep 16 16:46:06 2020 +0000
+++ b/test-data/1_codeml.ctl	Sat Nov 27 09:55:34 2021 +0000
@@ -1,7 +1,7 @@
 
-      seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_1.dat * sequence data file name
+      seqfile = /tmp/tmpag83k3gw/files/2/a/5/dataset_2a51ed5b-9c83-455a-bcf6-3f83c1505ff8.dat * sequence data file name
       outfile = run_codeml * main result file name
-     treefile = /tmp/tmpr0j4bmyj/files/000/dataset_2.dat * tree structure file name
+     treefile = /tmp/tmpag83k3gw/files/e/1/9/dataset_e195971f-e59d-4e2c-8b36-ab81d32476dc.dat * tree structure file name
         noisy = 9  * 0,1,2,3,9: how much rubbish on the screen
       verbose = 0  * 1: detailed output, 0: concise output
       runmode = 0  * 0: user tree;  1: semi-automatic;  2: automatic
@@ -35,7 +35,7 @@
         ncatG = 3  * # of categories in dG of NSsites models
       fix_rho = 1  * 0: estimate rho; 1: fix it at rho
           rho = 0.0 * initial or fixed rho,   0:no correlation
-        getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
+        getSE = 0  * 0: dont want them, 1: want S.E.s of estimates
  RateAncestor = 1  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
    Small_Diff = 5e-07
     cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
diff -r b2b8e75a962d -r f9cb3a4339c2 test-data/2_codeml.ctl
--- a/test-data/2_codeml.ctl	Wed Sep 16 16:46:06 2020 +0000
+++ b/test-data/2_codeml.ctl	Sat Nov 27 09:55:34 2021 +0000
@@ -1,7 +1,7 @@
 
-      seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_12.dat * sequence data file name
+      seqfile = /tmp/tmpag83k3gw/files/2/6/2/dataset_262fd0d9-9018-4668-992c-0ed4943f9168.dat * sequence data file name
       outfile = run_codeml * main result file name
-     treefile = /tmp/tmpr0j4bmyj/files/000/dataset_13.dat * tree structure file name
+     treefile = /tmp/tmpag83k3gw/files/c/2/b/dataset_c2b7d4a1-033d-4bd9-92ba-ad7936f0c09a.dat * tree structure file name
         noisy = 9  * 0,1,2,3,9: how much rubbish on the screen
       verbose = 0  * 1: detailed output, 0: concise output
       runmode = 0  * 0: user tree;  1: semi-automatic;  2: automatic
@@ -35,7 +35,7 @@
         ncatG = 3  * # of categories in dG of NSsites models
       fix_rho = 1  * 0: estimate rho; 1: fix it at rho
           rho = 0.0 * initial or fixed rho,   0:no correlation
-        getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
+        getSE = 0  * 0: dont want them, 1: want S.E.s of estimates
  RateAncestor = 1  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
    Small_Diff = 5e-07
     cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
diff -r b2b8e75a962d -r f9cb3a4339c2 test-data/3_codeml.ctl
--- a/test-data/3_codeml.ctl	Wed Sep 16 16:46:06 2020 +0000
+++ b/test-data/3_codeml.ctl	Sat Nov 27 09:55:34 2021 +0000
@@ -1,7 +1,7 @@
 
-      seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_23.dat * sequence data file name
+      seqfile = /tmp/tmpag83k3gw/files/9/9/6/dataset_99661b4e-1dc8-471d-9db3-6eb3d2655fbe.dat * sequence data file name
       outfile = run_codeml * main result file name
-     treefile = /tmp/tmpr0j4bmyj/files/000/dataset_24.dat * tree structure file name
+     treefile = /tmp/tmpag83k3gw/files/d/4/d/dataset_d4d2b602-4042-48d7-9636-abdf169513fa.dat * tree structure file name
         noisy = 9  * 0,1,2,3,9: how much rubbish on the screen
       verbose = 0  * 1: detailed output, 0: concise output
       runmode = 0  * 0: user tree;  1: semi-automatic;  2: automatic
@@ -35,7 +35,7 @@
         ncatG = 3  * # of categories in dG of NSsites models
       fix_rho = 1  * 0: estimate rho; 1: fix it at rho
           rho = 0.0 * initial or fixed rho,   0:no correlation
-        getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
+        getSE = 0  * 0: dont want them, 1: want S.E.s of estimates
  RateAncestor = 1  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
    Small_Diff = 5e-07
     cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?