Repository 'raxml'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/raxml

Changeset 7:b1e68bbe4cef (2023-11-18)
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
b
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
b
@@ -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'
b
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;