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diff raxml.xml @ 24:c9fd05a8751e draft

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planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty
author tiagoantao
date Sat, 07 Nov 2015 16:10:49 -0500
parents dc9a86a5d97e
children 2d9f1ef9b5cc
line wrap: on
line diff
--- a/raxml.xml	Tue Nov 03 16:15:13 2015 -0500
+++ b/raxml.xml	Sat Nov 07 16:10:49 2015 -0500
@@ -5,7 +5,6 @@
   </requirements>
   <command interpreter="python">raxml.py
     ## Required parameters 
-    ## Program name and threads are hard-coded as they are dependent on the binary and threads are specified in the Galaxy's tool configuration
     ## binary is hard-coded to the pthreads enabled raxml executable
     --binary "raxmlHPC-PTHREADS"
     ## (-T)
@@ -230,7 +229,7 @@
             </param>
         </when>
     </conditional>
-    <param name="random_seed" type="integer" value="1234567890" size="12" label="Random
+    <param name="random_seed" type="integer" value="1234567890" label="Random
         seed used for the parsimony inferences" />
     <conditional name="selExtraOpts">
         <param name="extraOptions" type="select" label="RAxML options to use"
@@ -241,7 +240,7 @@
         </param>
         <when value="full">
             ## (-N/#)
-            <param name="number_of_runs" type="integer" size="8" value=""
+            <param name="number_of_runs" type="integer" value=""
                 label="Number of runs" help="Specify the number of
                 alternative runs (-N|#) on distinct starting trees In combination
                 with the '-b' option will invoke a multiple boostrap analysis.
@@ -279,20 +278,20 @@
                 <option value="S16B">S16B</option>
             </param>
             ## (-b)
-            <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping" refresh_on_change='true'  optional="True" />
+            <param name="bootseed" type="integer" value="" label="Random number for non-parametric bootstrapping" refresh_on_change='true'  optional="True" />
             ## (-x)
-            <param name="rapid_bootstrap_random_seed" type="integer" value='' size="7" label="Rapid bootstrapping random seed" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." />
+            <param name="rapid_bootstrap_random_seed" type="integer" value='' label="Rapid bootstrapping random seed" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." />
             ## (-B)
-            <param name="cutoff_threshold" type="float" size="8" label="MR Cutoff threshold" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" />
+            <param name="cutoff_threshold" type="float" label="MR Cutoff threshold" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" />
             ## (-c)
-            <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" />
+            <param name="numofcats" type="integer" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" />
                 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now.
             ## (-d)
             <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="--search_complete_random_tree" falsevalue="" display="checkboxes" label="Start ML optimization from a complete random starting tree" />
             ## (-D)
             <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" label="ML search convergence criterion" />
             ## (-e)
-            <param name="model_opt_precision" type="float" size="8" label="Model optimization precision" value="" help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used" optional="True" />
+            <param name="model_opt_precision" type="float" label="Model optimization precision" value="" help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used" optional="True" />
             ## (-E)
             <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" />
             ## (-f)
@@ -328,11 +327,11 @@
             ## (-g)
             <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" />
             ## (-G)
-            <param name="enable_evol_heuristics" type="float" size="8" label="Enable the ML-based evolutionary placement algorithm heuristics" help="Enable the ML-based evolutionary placement algorithm heuristics by specifiyng a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)." optional="True" >
+            <param name="enable_evol_heuristics" type="float" label="Enable the ML-based evolutionary placement algorithm heuristics" help="Enable the ML-based evolutionary placement algorithm heuristics by specifiyng a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)." optional="True" >
                 <validator type="in_range" message="0.0 &lt;= fraction &lt;= 1.0" min="0.0" max="1.0"/>
             </param>
             ## (-i)
-            <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting" optional="True" />
+            <param name="initial_rearrangement_setting" type="integer" value="" label="Initial rearrangement setting" optional="True" />
             ## (-I)
             <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True">
                 <option value="" selected="True"></option>
@@ -365,7 +364,7 @@
             <param name="estimate_individual_branch_lengths" type="boolean" checked="no" truevalue="--estimate_individual_branch_lengths" falsevalue="" display="checkboxes" label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file (-q)." optional="True" />
             ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files
             ## (-o)
-            <param name="outgroup_name" type="text" size="40" value="" label="Outgroup name" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" />
+            <param name="outgroup_name" type="text" value="" label="Outgroup name" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" />
             ## (-O)
             <param name="disable_undetermined_seq_check" type="boolean" checked="no" truevalue="--disable_undertermined_seq_check" falsevalue="" display="checkboxes" label="Disable check for completely undetermined sequence in alignment" optional="True" help="Disable the check for completely undetermined sequence in alignment. The program will not exit with an error message when '-O' is specified." />
             <param name="external_protein_model" format="txt" type="data" label="External AA substitution model" help="Specify the file name of a user-defined AA (Protein) substitution model. This file must contain 420 entries, the first 400 being the AA substitution rates (this must be a symmetric matrix) and the last 20 are the empirical base frequencies." optional="True" />
@@ -387,7 +386,7 @@
             ## (-V)
             <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="--disable_raite_heterogeneity" falsevalue="" display="checkboxes" label="Disable rate heterogeneity" help="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead. Only works if you specify the CAT model of rate heterogeneity." optional="True" />
             ## (-W)
-            <param name="sliding_window_size" type="integer" size="5" value="" label="Sliding window size" optional="True" help="Sliding window size for leave-one-out site-specific placement bias algorithm. Only effective when used in combination with '-f S'. Default is '100 sites'" />
+            <param name="sliding_window_size" type="integer" value="" label="Sliding window size" optional="True" help="Sliding window size for leave-one-out site-specific placement bias algorithm. Only effective when used in combination with '-f S'. Default is '100 sites'" />
             ## (-x) - see it by the (-b)
             ## (-y)
             <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes" label="Compute a randomized parsimony starting tree only" optional="True" help="If you want to only compute a parsimony starting tree with RAxML specify '-y'. The program will exit after computation of the starting tree." />
@@ -403,29 +402,29 @@
             <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
             <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
         </data>
-        <data format="txt" name="bestTreeReq" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
+        <data format="nhx" name="bestTreeReq" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
             <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
         </data>
-        <data format="txt" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
+        <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
             <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
             <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
         </data>
-        <data format="txt" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
+        <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
             <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
             <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
         </data>
       ## ADVANCED
-        <data format="txt" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
+        <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
             <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
             <filter>selExtraOpts['extraOptions'] == "full"</filter>
         </data>
-        <data format="txt" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
+        <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
             <filter>(selExtraOpts['extraOptions'] == 'full')</filter>
             <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '' or selExtraOpts['bootseed'] == '') and (selExtraOpts['search_algorithm'] == 'a')</filter>
             <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
             <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter>
         </data>
-        <data format="txt" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
+        <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
             <filter>(selExtraOpts['extraOptions'] == "full")</filter>
             <filter>(selExtraOpts['multiple_model'] != '')</filter>
         </data>
@@ -441,7 +440,7 @@
             <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
             <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
         </data>
-        <data format="txt" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
+        <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
             <filter>(selExtraOpts['extraOptions'] == "full")</filter>
             <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
             <filter>selExtraOpts['bootseed'] == ''</filter> 
@@ -453,7 +452,7 @@
             <filter>(selExtraOpts['extraOptions'] == "full")</filter>
             <filter>(selExtraOpts['multiple_model'] is not None)</filter>
         </data>
-        <data format="txt" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
+        <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
             <filter>(selExtraOpts['extraOptions'] == "full")</filter>
             <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
             <filter>(selExtraOpts['bootseed'] == '')</filter> 
@@ -464,7 +463,7 @@
             <filter>(selExtraOpts['start_tree_file'] is None)</filter>
             <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
         </data>
-        <data format="txt" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
+        <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
             <filter>selExtraOpts['extraOptions'] == "full"</filter>
             <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
             <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
@@ -477,15 +476,15 @@
             <filter>selExtraOpts['extraOptions'] == "full"</filter>
             <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
         </data>
-        <data format="txt" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
+        <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
             <filter>selExtraOpts['extraOptions'] == "full"</filter>
             <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter>
         </data>
-        <data format="txt" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
+        <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
             <filter>selExtraOpts['extraOptions'] == "full"</filter>
             <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter>
         </data>
-        <data format="txt" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
+        <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
             <filter>selExtraOpts['extraOptions'] == "full"</filter>
             <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter>
         </data>
@@ -515,16 +514,25 @@
               </assert_contents>
           </output>
       </test>
+      <test>
+          <param name="extraOptions" value="full"/>
+          <param name="infile" value="dna.fasta"/>
+          <param name="model_type" value="nucleotide"/>
+          <param name="base_model" value="GTRCAT"/>
+          <param name="number_of_runs" value="5"/>
+          <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy">
+          <output name="bestTreeReq"/>
+              <assert_contents>
+                <has_text_matching expression="Frog" />
+              </assert_contents>
+          </output>
+      </test>
   </tests>
   <help>
 Title:
 ______
 Randomized Axelerated Maximum Likelihood
 
-Author:
-_______
-Alexandros Stamatakis 
-
 Description:
 ____________
 
@@ -533,8 +541,6 @@
 extremely large datasets, either in terms of the number of taxa and/or the
 sequence length.
 
-This wrapper works with the RAxML version 8.2.4.
-
 URL:
 ____
 Author's page: http://www.exelixis-lab.org/
@@ -547,9 +553,9 @@
 Oleksandr Moskalenko with adaptations from Tiago Antao.
 
   </help>
-<citations>
-  <citation type="doi">10.1093/bioinformatics/btu033</citation>
-  <citation type="bibtex">
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu033</citation>
+    <citation type="bibtex">
 @article{stamatakis2014raxml,
   title={RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies},
   author={Stamatakis, Alexandros},
@@ -559,6 +565,6 @@
   pages={1312--1313},
   year={2014},
   publisher={Oxford Univ Press}}
-  </citation>
-</citations>
+    </citation>
+  </citations>
 </tool>