# HG changeset patch
# User iuc
# Date 1525254248 14400
# Node ID ba71e26d5bdc4956e139716455213600ad3ca37a
# Parent  961a712f974319b84137e7c7cbee8776c6eff2fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 43935edeb0abb95b08b191b379e160ec25cb33c0

diff -r 961a712f9743 -r ba71e26d5bdc codeml.xml
--- a/codeml.xml	Tue Aug 29 19:12:01 2017 -0400
+++ b/codeml.xml	Wed May 02 05:44:08 2018 -0400
@@ -14,11 +14,9 @@
     <version_command><![CDATA[ codeml /dev/null 2>&1 | tail -1 ]]></version_command>
 
     <command><![CDATA[
-
 codeml '$codeml_ctl'
 &&
 mv '$codeml_ctl' '$ctl'
-
     ]]></command>
 
     <configfiles>
@@ -65,12 +63,10 @@
     cleandata = $adv.cleandata  * remove sites with ambiguity data (1:yes, 0:no)?
   fix_blength = $adv.fix_blength   * 0: ignore, -1: random, 1: initial, 2: fixed
        method = $adv.method   * 0: simultaneous; 1: one branch at a time
-
         ]]></configfile>
     </configfiles>
 
     <inputs>
-
         <param name="concat_nuc" type="data" format="fasta" label="Sequences file" help="The fasta file with the sequences to be analyzed" />
         <param name="tree" type="data" format="nhx" label="tree file" help="Tree file in Newick format" />
 
@@ -314,18 +310,17 @@
     </tests>
 
     <help><![CDATA[
-
 .. class:: infomark
 
 **Galaxy integration** Victor Mataigne and ABIMS TEAM.
 
- Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
+Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
 
 ----------
 
 **CompCodeML (from paml package)**
 
-A few help is detailed below ; full and detailed codeml readme can be found on the paml website_
+A few help is detailed below ; full and detailed codeml readme can be found on the paml website_.
 
 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
 
@@ -334,6 +329,7 @@
 Due to their high number, some parameters incompatibility can remain.
 
 This Galaxy implementation :
+
 - handles incompatibilities between branch and sites models (the tool CANNOT be run with incompatible models).
 - warns the user in a help section when an advanced parameter has known incompatibilities (the tool CAN be run, but the output files will be empty).
 
@@ -342,11 +338,12 @@
 .. class:: infomark
 
 Known incompatibilities:
-    - 'seqtype' = 3 : only compatible with 'FSsites' = 0.
-    - 'clock' = 2 : needs branch labels in the tree.
-    - fix_alpha !=1 combined with alpha !=0 are not compatible with NSsites !=0
-    - 'aaDist' = 0 is the only one compatible with 'NSsites' different than 0 and 'seqtype' = 1.
-    - 'method' = 1 : does not work with 'clock' different than 0.
+
+- 'seqtype' = 3 : only compatible with 'FSsites' = 0.
+- 'clock' = 2 : needs branch labels in the tree.
+- fix_alpha !=1 combined with alpha !=0 are not compatible with NSsites !=0
+- 'aaDist' = 0 is the only one compatible with 'NSsites' different than 0 and 'seqtype' = 1.
+- 'method' = 1 : does not work with 'clock' different than 0.
 
 ----------
 
@@ -368,10 +365,12 @@
 **Parameters**
 
 Several models are available.
+
 - branch models ("model" parameter).
 - sites models ("NSsites" parameter, model is left at 0).
 - branch-sites models (when model = 2 NSsites=2,3).
 - Clade models (when model=3 NSsites=2,3).
+
 Basically, this tool write a configfile called codeml.ctl with the specified parameters and then launches codeml.
 
 .. class:: infomark
@@ -384,10 +383,12 @@
 
 How to run the branch-site models (A &amp; B in Yang &amp; Nielsen 2002 MBE) ?
 The options are :
-    Model A: (model=2, NSsites=2).
-    Model B: (model=2, NSsites=3).
+
+- Model A: (model=2, NSsites=2).
+- Model B: (model=2, NSsites=3).
 
 How to run the M0 (one-ratio) model :
+
     model = 0, NSsites= = 0.
 
 ----------
@@ -396,27 +397,35 @@
 
 .. class:: infomark
 
-See paml complete manual and FAQ on paml website_
+See paml complete manual and FAQ on the paml website_.
 
 .. _website: http://abacus.gene.ucl.ac.uk/software/paml.html
 
 **Details of some parameters :**
 
-    - 'kappa' denotes the transition/transversion rate ratio.
-    - 'fix_kappa' specifies whether kappa in K80, F84, or HKY85 is given at a fixed value or is to be estimated by iteration from the data.
-        -> If fix_kappa = 1 (fixed), the value of kappa is the given value
-        -> If fix_kappa = 0 (estimated) the value of kappa is used as the initial estimate for iteration.
+- 'kappa' denotes the transition/transversion rate ratio.
+- 'fix_kappa' specifies whether kappa in K80, F84, or HKY85 is given at a fixed value or is to be estimated by iteration from the data.
+
+  -> If fix_kappa = 1 (fixed), the value of kappa is the given value
+
+  -> If fix_kappa = 0 (estimated) the value of kappa is used as the initial estimate for iteration.
+
+- 'alpha' refers to the shape parameter alpha of the gamma distribution for variable substitution rates across sites (Yang 1994a).
+- 'fix_alpha' works in a similar way that fix_kappa.
+
+  -> The model of a single rate for all sites is specified as fix_alpha = 1 and alpha = 0 (0 means infinity)
 
-    - 'alpha' refers to the shape parameter alpha of the gamma distribution for variable substitution rates across sites (Yang 1994a).
-    - 'fix_alpha' works in a similar way that fix_kappa.
-        -> The model of a single rate for all sites is specified as fix_alpha = 1 and alpha = 0 (0 means infinity)
-        -> The (discrete-) gamma model is specified by a positive value for alpha, and 'ncatG' is then the number of categories for the discrete-gamma model. Values such as 5, 4, 8, or 10 are reasonable.
+  -> The (discrete-) gamma model is specified by a positive value for alpha, and 'ncatG' is then the number of categories for the discrete-gamma model. Values such as 5, 4, 8, or 10 are reasonable.
+
+- fix_rho and rho work in a similar way and concern independence or correlation of rates at adjacent sites, where rho is the correlation parameter of the auto-discrete-gamma model (Yang 1995).
+
+  -> The model of independent rates for sites is specified as fix_rho = 1 and rho = 0; choosing alpha = 0 further means a constant rate for all sites.
 
-    - fix_rho and rho work in a similar way and concern independence or correlation of rates at adjacent sites, where rho is the correlation parameter of the auto-discrete-gamma model (Yang 1995).
-        -> The model of independent rates for sites is specified as fix_rho = 1 and rho = 0; choosing alpha = 0 further means a constant rate for all sites.
-        -> The auto-discrete-gamma model is specified by positive values for both alpha and rho.
-        -> The model of a constant rate for sites is a special case of the (discrete) gamma model with alpha = 0 (means infinity).
-        -> The model of independent rates for sites is a special case of the auto-discrete-gamma model with rho = 0.
+  -> The auto-discrete-gamma model is specified by positive values for both alpha and rho.
+
+  -> The model of a constant rate for sites is a special case of the (discrete) gamma model with alpha = 0 (means infinity).
+
+  -> The model of independent rates for sites is a special case of the auto-discrete-gamma model with rho = 0.
 
 ----------
 
@@ -434,18 +443,16 @@
 
 Some models implemented in codeml allow several groups of branches on the tree, which are assigned different parameters of interest.
 
-    - For example, in the local clock models (clock = 2 or 3), you can have, say, 3 branch rate groups, with low, medium, and high rates respectively.
-
-    - Also the branch-specific codon models (model = 2 or 3 or codonml) allow different branch groups to have different ωs, leading to so called “two-ratios” and “three-ratios” models.
-
-    - All those models require branches or nodes in the tree to be labeled. Branch labels are specified in the same way as branch lengths except that the symbol “#” is used rather than “:”. The branch labels are consecutive integers starting from 0, which is the default and does not have to be specified.
+- For example, in the local clock models (clock = 2 or 3), you can have, say, 3 branch rate groups, with low, medium, and high rates respectively.
+- Also the branch-specific codon models (model = 2 or 3 or codonml) allow different branch groups to have different ωs, leading to so called “two-ratios” and “three-ratios” models.
+- All those models require branches or nodes in the tree to be labeled. Branch labels are specified in the same way as branch lengths except that the symbol “#” is used rather than “:”. The branch labels are consecutive integers starting from 0, which is the default and does not have to be specified.
 
 In ((Hsa_Human, Hla_gibbon) #1, ((Cgu/Can_colobus, Pne_langur), Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); :
     The internal branch ancestral to human and gibbon has the ratio ω1, while all other branches (with the default label #0) have the background ratio ω0.
 
-The following trees are equivalent :
-    ((rabbit, rat) $1, human), goat_cow, marsupial);
-    (((rabbit #1, rat #1) #1, human), goat_cow, marsupial);
+The following trees are equivalent:
+- ((rabbit, rat) $1, human), goat_cow, marsupial);
+- (((rabbit #1, rat #1) #1, human), goat_cow, marsupial);
 
 $ is the symbol for clade labels.
 
@@ -455,8 +462,6 @@
     $1 is first applied to the whole clade of placental mammals (except for the human lineage), and then $2 is applied to the rabbit-rat clade.
     Equivalent tree with only '#' :
     ((((rabbit #2, rat #2) #2, human #3) #1, goat_cow #1) #1, marsupial);
-
-
     ]]></help>
 
     <citations>
diff -r 961a712f9743 -r ba71e26d5bdc test-data/1_codeml.ctl
--- a/test-data/1_codeml.ctl	Tue Aug 29 19:12:01 2017 -0400
+++ b/test-data/1_codeml.ctl	Wed May 02 05:44:08 2018 -0400
@@ -1,7 +1,7 @@
 
-      seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_1.dat * sequence data file name
+      seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_1.dat * sequence data file name
       outfile = run_codeml * main result file name
-     treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_2.dat * tree structure file name
+     treefile = /tmp/tmpr0j4bmyj/files/000/dataset_2.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
@@ -41,5 +41,4 @@
     cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
   fix_blength = 0   * 0: ignore, -1: random, 1: initial, 2: fixed
        method = 0   * 0: simultaneous; 1: one branch at a time
-
         
\ No newline at end of file
diff -r 961a712f9743 -r ba71e26d5bdc test-data/2_codeml.ctl
--- a/test-data/2_codeml.ctl	Tue Aug 29 19:12:01 2017 -0400
+++ b/test-data/2_codeml.ctl	Wed May 02 05:44:08 2018 -0400
@@ -1,7 +1,7 @@
 
-      seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_12.dat * sequence data file name
+      seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_12.dat * sequence data file name
       outfile = run_codeml * main result file name
-     treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_13.dat * tree structure file name
+     treefile = /tmp/tmpr0j4bmyj/files/000/dataset_13.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
@@ -41,5 +41,4 @@
     cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
   fix_blength = 0   * 0: ignore, -1: random, 1: initial, 2: fixed
        method = 0   * 0: simultaneous; 1: one branch at a time
-
         
\ No newline at end of file
diff -r 961a712f9743 -r ba71e26d5bdc test-data/3_codeml.ctl
--- a/test-data/3_codeml.ctl	Tue Aug 29 19:12:01 2017 -0400
+++ b/test-data/3_codeml.ctl	Wed May 02 05:44:08 2018 -0400
@@ -1,7 +1,7 @@
 
-      seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_23.dat * sequence data file name
+      seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_23.dat * sequence data file name
       outfile = run_codeml * main result file name
-     treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_24.dat * tree structure file name
+     treefile = /tmp/tmpr0j4bmyj/files/000/dataset_24.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
@@ -41,5 +41,4 @@
     cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
   fix_blength = 0   * 0: ignore, -1: random, 1: initial, 2: fixed
        method = 0   * 0: simultaneous; 1: one branch at a time
-
         
\ No newline at end of file