Mercurial > repos > iuc > raxml
changeset 7:b1e68bbe4cef draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit ca98a256623d6636805d6fbc4ff85fb7465b2f90
| author | iuc |
|---|---|
| date | Sat, 18 Nov 2023 23:18:58 +0000 |
| parents | ea30d3089354 |
| children | |
| files | raxml.py raxml.xml test-data/RAxML_parsimonyTree.galaxy.multi |
| diffstat | 3 files changed, 62 insertions(+), 77 deletions(-) [+] |
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--- a/raxml.py Sat Nov 05 17:42:11 2022 +0000 +++ b/raxml.py Sat Nov 18 23:18:58 2023 +0000 @@ -85,12 +85,6 @@ with open('RAxML_resultPartitions.galaxy', 'w') as outfile: outfile.write("No partition files were produced.\n") - # DEBUG options - with open('RAxML_info.galaxy', 'a') as infof: - infof.write('\nOM: CLI options DEBUG START:\n') - infof.write(options.__repr__()) - infof.write('\nOM: CLI options DEBUG END\n') - if __name__ == "__main__": __main__()
--- a/raxml.xml Sat Nov 05 17:42:11 2022 +0000 +++ b/raxml.xml Sat Nov 18 23:18:58 2023 +0000 @@ -1,8 +1,8 @@ -<tool id="raxml" name="Phyogenetic reconstruction with RAxML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>- Maximum Likelihood based inference of large phylogenetic trees</description> +<tool id="raxml" name="RAxML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> + <description>Maximum Likelihood based inference of large phylogenetic trees</description> <macros> <token name="@TOOL_VERSION@">8.2.12</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <xrefs> <xref type="bio.tools">raxml</xref> @@ -346,137 +346,129 @@ </conditional> </inputs> <outputs> - <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" /> + <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="${tool.name} on ${on_string}: Info" /> <!-- REQUIRED --> - <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log"> - <filter>selExtraOpts['extraOptions'] == 'required'</filter> - <filter>selExtraOpts['search_algorithm'] != 'a'</filter> + <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="${tool.name} on ${on_string}: Log"> + <filter>selExtraOpts['extraOptions'] == 'required' or (selExtraOpts['extraOptions'] == "full" and selExtraOpts['rapid_bootstrap_random_seed'] == '' and selExtraOpts['bootseed'] == '' and selExtraOpts['search_algorithm'] != 'a' and selExtraOpts['search_algorithm'] != 'b' and not selExtraOpts['majority_rule_consensus'])</filter> </data> - <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> - <filter>selExtraOpts['extraOptions'] == 'required'</filter> - <filter>selExtraOpts['search_algorithm'] != 'a'</filter> + + <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="${tool.name} on ${on_string}: Parsimony Tree"> + <filter>selExtraOpts['extraOptions'] != "required" or selExtraOpts['search_algorithm'] != 'a'</filter> </data> - <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result"> - <filter>selExtraOpts['extraOptions'] == 'required'</filter> - <filter>selExtraOpts['search_algorithm'] != 'a'</filter> + <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="${tool.name} on ${on_string}: Result"> + <filter>selExtraOpts['extraOptions'] == 'required' or (selExtraOpts['extraOptions'] == "full" and selExtraOpts['rapid_bootstrap_random_seed'] == '' and selExtraOpts['bootseed'] == '' and selExtraOpts['search_algorithm'] != 'a' and selExtraOpts['search_algorithm'] != 'b' and not selExtraOpts['majority_rule_consensus'])</filter> </data> <!-- ADVANCED --> - <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree"> + <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="${tool.name} on ${on_string}: Random Tree"> <filter>selExtraOpts['search_complete_random_tree'] is True</filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> - <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> - <!-- <filter>selExtraOpts['extraOptions'] == 'full'</filter> --> - <!-- <filter>selExtraOpts['search_algorithm'] != 'b'</filter> - <filter>not selExtraOpts['majority_rule_consensus']</filter> --> - </data> - <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> - <filter>selExtraOpts['extraOptions'] == "full"</filter> - <filter>selExtraOpts['multiple_model'] != ''</filter> - </data> - <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions"> + <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="${tool.name} on ${on_string}: Best-scoring ML Tree"/> + + <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="${tool.name} on ${on_string}: Best-scoring ML Tree Partitions"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['multiple_model'] is not None </filter> </data> - <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log"> - <filter>selExtraOpts['extraOptions'] == "full"</filter> - <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter> - <filter>selExtraOpts['bootseed'] == ''</filter> - <filter>selExtraOpts['search_algorithm'] != 'a'</filter> - <filter>selExtraOpts['search_algorithm'] != 'b'</filter> - <filter>not selExtraOpts['majority_rule_consensus']</filter> - </data> - <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result"> - <filter>selExtraOpts['extraOptions'] == "full"</filter> - <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter> - <filter>selExtraOpts['bootseed'] == ''</filter> - <filter>selExtraOpts['search_algorithm'] != 'a'</filter> - <filter>selExtraOpts['search_algorithm'] != 'b'</filter> - <filter>not selExtraOpts['majority_rule_consensus']</filter> - </data> - <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions"> + + <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="${tool.name} on ${on_string}: Result Partitions"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['multiple_model'] is not None</filter> </data> - <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> - <filter>selExtraOpts['extraOptions'] == "full"</filter> - <!-- - <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter> - <filter>selExtraOpts['bootseed'] == ''</filter> - <filter>selExtraOpts['search_algorithm'] != 'a'</filter> - <filter>selExtraOpts['constraint_file'] is None</filter> - <filter>selExtraOpts['groupingfile'] is None</filter> - <filter>selExtraOpts['search_complete_random_tree'] is False</filter> - <filter>selExtraOpts['start_tree_file'] is None</filter> - <filter>not selExtraOpts['majority_rule_consensus'] == ''</filter> - --> - </data> - <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees"> + + <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="${tool.name} on ${on_string}: Final Bootstrap Trees"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter> <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter> </data> - <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions"> + <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="${tool.name} on ${on_string}: Bipartitions"> <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> - <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels"> + <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="${tool.name} on ${on_string}: Bipartitions Branch Labels"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter> </data> - <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree"> + <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="${tool.name} on ${on_string}: Strict Consensus Tree"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['majority_rule_consensus'] == 'STRICT'</filter> </data> - <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree"> + <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="${tool.name} on ${on_string}: Majority Rule Consensus Tree"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['majority_rule_consensus'] == 'MR'</filter> </data> - <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree"> + <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="${tool.name} on ${on_string}: Majority Rule Extended Consensus Tree"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['majority_rule_consensus'] == 'MRE'</filter> </data> - <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences."> + <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="${tool.name} on ${on_string}: Pair-wise bipartition frequences."> <filter>selExtraOpts['search_algorithm'] == 'm' </filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> - <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores"> + <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="${tool.name} on ${on_string}: Per-site likelihood schores"> <filter>selExtraOpts['search_algorithm'] == 'g' </filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> - <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances"> + <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="${tool.name} on ${on_string}: Pair-wise distances"> <filter>selExtraOpts['search_algorithm'] == 'x' </filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> </outputs> <tests> - <test> + <test expect_num_outputs="5"> <param name="extraOptions" value="required"/> <param name="infile" value="dna.phy"/> <param name="model_type" value="nucleotide"/> <param name="base_model" value="GTRCAT"/> - <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" /> + <output name="info"> + <assert_contents><has_text text="Overall execution time"/></assert_contents> + </output> + <output name="log"> + <assert_contents> + <has_n_columns n="2" sep=" "/> + <has_n_lines n="9"/> + </assert_contents> + </output> + <output name="parsimonyTree" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" /> + <output name="result" ftype="nhx"> + <assert_contents><has_text text="Frog"/></assert_contents> + </output> <output name="bestTree" ftype="nhx"> <assert_contents> <has_text_matching expression="Frog" /> </assert_contents> </output> </test> - <test> + <test expect_num_outputs="5"> <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="parsimonyTree" ftype="nhx"> + <output name="info"> + <assert_contents><has_text text="Overall execution time"/></assert_contents> + </output> + <output name="log"> <assert_contents> - <has_text_matching expression="Chicken" /> + <has_n_columns n="2" sep=" "/> + <has_n_lines n="41"/> </assert_contents> </output> - <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" ftype="nhx" compare="re_match"/> + <output name="result"> + <assert_contents> + <has_text_matching expression="Chicken" /> + <has_n_lines n="5"/> + </assert_contents> + </output> + <output name="parsimonyTree" ftype="nhx"> + <assert_contents> + <has_text text="(Whale,((((Mouse,Chicken),Human),Rat),((Frog,(Carp,Loach)),Seal)),Cow);"/> + <has_n_lines n="5"/> + </assert_contents> + </output> <output name="bestTree" ftype="nhx"> <assert_contents> - <has_text_matching expression="Whale" /> + <has_text text="Whale" /> + <has_text text="Chicken"/> </assert_contents> </output> </test>
--- a/test-data/RAxML_parsimonyTree.galaxy.multi Sat Nov 05 17:42:11 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -\(\(Whale:0.0000[0-9]*,\(\(\(Human:0.5359[0-9]*,Seal:0.0253[0-9]*\):0.2219[0-9]*,Frog:0.1028[0-9]*\):0.2186[0-9]*,\(Chicken:0.2075[0-9]*,\(Mouse:0.0833[0-9]*,Rat:0.0803[0-9]*\):0.0752[0-9]*\):0.1271[0-9]*\):0.0333[0-9]*\):0.1439[0-9]*,\(Carp:0.3512[0-9]*,Loach:0.0000[0-9]*\):0.2173[0-9]*,Cow:0.0625[0-9]*\):0.0;