Previous changeset 6:ea30d3089354 (2022-11-05) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit ca98a256623d6636805d6fbc4ff85fb7465b2f90 |
modified:
raxml.py raxml.xml |
removed:
test-data/RAxML_parsimonyTree.galaxy.multi |
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diff -r ea30d3089354 -r b1e68bbe4cef raxml.py --- a/raxml.py Sat Nov 05 17:42:11 2022 +0000 +++ b/raxml.py Sat Nov 18 23:18:58 2023 +0000 |
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@@ -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__() |
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diff -r ea30d3089354 -r b1e68bbe4cef raxml.xml --- a/raxml.xml Sat Nov 05 17:42:11 2022 +0000 +++ b/raxml.xml Sat Nov 18 23:18:58 2023 +0000 |
[ |
b'@@ -1,8 +1,8 @@\n-<tool id="raxml" name="Phyogenetic reconstruction with RAxML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n- <description>- Maximum Likelihood based inference of large phylogenetic trees</description>\n+<tool id="raxml" name="RAxML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">\n+ <description>Maximum Likelihood based inference of large phylogenetic trees</description>\n <macros>\n <token name="@TOOL_VERSION@">8.2.12</token>\n- <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n </macros>\n <xrefs>\n <xref type="bio.tools">raxml</xref>\n@@ -346,137 +346,129 @@\n </conditional>\n </inputs>\n <outputs>\n- <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />\n+ <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="${tool.name} on ${on_string}: Info" />\n <!-- REQUIRED -->\n- <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">\n- <filter>selExtraOpts[\'extraOptions\'] == \'required\'</filter>\n- <filter>selExtraOpts[\'search_algorithm\'] != \'a\'</filter>\n+ <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="${tool.name} on ${on_string}: Log">\n+ <filter>selExtraOpts[\'extraOptions\'] == \'required\' or (selExtraOpts[\'extraOptions\'] == "full" and selExtraOpts[\'rapid_bootstrap_random_seed\'] == \'\' and selExtraOpts[\'bootseed\'] == \'\' and selExtraOpts[\'search_algorithm\'] != \'a\' and selExtraOpts[\'search_algorithm\'] != \'b\' and not selExtraOpts[\'majority_rule_consensus\'])</filter>\n </data>\n- <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">\n- <filter>selExtraOpts[\'extraOptions\'] == \'required\'</filter>\n- <filter>selExtraOpts[\'search_algorithm\'] != \'a\'</filter>\n+\n+ <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="${tool.name} on ${on_string}: Parsimony Tree">\n+ <filter>selExtraOpts[\'extraOptions\'] != "required" or selExtraOpts[\'search_algorithm\'] != \'a\'</filter>\n </data>\n- <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">\n- <filter>selExtraOpts[\'extraOptions\'] == \'required\'</filter>\n- <filter>selExtraOpts[\'search_algorithm\'] != \'a\'</filter>\n+ <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="${tool.name} on ${on_string}: Result">\n+ <filter>selExtraOpts[\'extraOptions\'] == \'required\' or (selExtraOpts[\'extraOptions\'] == "full" and selExtraOpts[\'rapid_bootstrap_random_seed\'] == \'\' and selExtraOpts[\'bootseed\'] == \'\' and selExtraOpts[\'search_algorithm\'] != \'a\' and selExtraOpts[\'search_algorithm\'] != \'b\' and not selExtraOpts[\'majority_rule_consensus\'])</filter>\n </data>\n <!-- ADVANCED -->\n- <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">\n+ <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="${tool.name} on ${on_string}: Random Tree">\n <filter>selExtraOpts[\'search_complete_random_tree\'] is True</filter>\n <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n </data>\n- <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">\n- <!-- <filter>selExtraOpts[\'extraOptions\'] == \'full\'</filter> -->\n- <!-- <filter>selExtraOpts[\'search_algorithm\'] != \'b\'</filter>\n- <filter>not selExtraOpts[\'majority_rule_consensus\']</filter> -->\n- </data>\n- <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">\n- <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n- <filter>selExtraOpts[\'multiple_model\'] != \'\'</fi'..b'm\'] == \'m\' </filter>\n <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n </data>\n- <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">\n+ <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="${tool.name} on ${on_string}: Per-site likelihood schores">\n <filter>selExtraOpts[\'search_algorithm\'] == \'g\' </filter>\n <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n </data>\n- <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">\n+ <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="${tool.name} on ${on_string}: Pair-wise distances">\n <filter>selExtraOpts[\'search_algorithm\'] == \'x\' </filter>\n <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n </data>\n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="5">\n <param name="extraOptions" value="required"/>\n <param name="infile" value="dna.phy"/>\n <param name="model_type" value="nucleotide"/>\n <param name="base_model" value="GTRCAT"/>\n- <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" />\n+ <output name="info">\n+ <assert_contents><has_text text="Overall execution time"/></assert_contents>\n+ </output>\n+ <output name="log">\n+ <assert_contents>\n+ <has_n_columns n="2" sep=" "/>\n+ <has_n_lines n="9"/>\n+ </assert_contents>\n+ </output>\n+ <output name="parsimonyTree" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" />\n+ <output name="result" ftype="nhx">\n+ <assert_contents><has_text text="Frog"/></assert_contents>\n+ </output>\n <output name="bestTree" ftype="nhx">\n <assert_contents>\n <has_text_matching expression="Frog" />\n </assert_contents>\n </output>\n </test>\n- <test>\n+ <test expect_num_outputs="5">\n <param name="extraOptions" value="full"/>\n <param name="infile" value="dna.fasta"/>\n <param name="model_type" value="nucleotide"/>\n <param name="base_model" value="GTRCAT"/>\n <param name="number_of_runs" value="5"/>\n- <output name="parsimonyTree" ftype="nhx">\n+ <output name="info">\n+ <assert_contents><has_text text="Overall execution time"/></assert_contents>\n+ </output>\n+ <output name="log">\n <assert_contents>\n- <has_text_matching expression="Chicken" />\n+ <has_n_columns n="2" sep=" "/>\n+ <has_n_lines n="41"/>\n </assert_contents>\n </output>\n- <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" ftype="nhx" compare="re_match"/>\n+ <output name="result">\n+ <assert_contents>\n+ <has_text_matching expression="Chicken" />\n+ <has_n_lines n="5"/>\n+ </assert_contents>\n+ </output>\n+ <output name="parsimonyTree" ftype="nhx">\n+ <assert_contents>\n+ <has_text text="(Whale,((((Mouse,Chicken),Human),Rat),((Frog,(Carp,Loach)),Seal)),Cow);"/>\n+ <has_n_lines n="5"/>\n+ </assert_contents>\n+ </output>\n <output name="bestTree" ftype="nhx">\n <assert_contents>\n- <has_text_matching expression="Whale" />\n+ <has_text text="Whale" />\n+ <has_text text="Chicken"/>\n </assert_contents>\n </output>\n </test>\n' |
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diff -r ea30d3089354 -r b1e68bbe4cef test-data/RAxML_parsimonyTree.galaxy.multi --- 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; |