| Previous changeset 1:288db50d1fb9 (2017-11-25) Next changeset 3:973a28be3b7f (2020-01-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91 |
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modified:
iqtree.xml |
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added:
iqtree_macros.xml |
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| diff -r 288db50d1fb9 -r d1c340a5664b iqtree.xml --- a/iqtree.xml Sat Nov 25 18:17:09 2017 -0500 +++ b/iqtree.xml Wed Oct 17 11:43:10 2018 -0400 |
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| @@ -1,8 +1,9 @@ -<tool id="iqtree" name="IQ-TREE" version="1.5.5.1" > +<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@.1" > <description>Phylogenomic / evolutionary tree construction from multiple sequences</description> - <requirements> - <requirement type="package" version="1.5.5">iqtree</requirement> - </requirements> + <macros> + <import>iqtree_macros.xml</import> + </macros> + <expand macro="requirements" /> <command detect_errors='exit_code' ><![CDATA[ iqtree -pre PREF @@ -362,9 +363,8 @@ </conditional> <param argument="-rcluster" type="integer" optional="true" label="Specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014)" help="This is similar to --rcluster-percent option of PartitionFinder. For example, with -rcluster 10 only the top 10% partition schemes are considered to save computations." /> <param argument="-mset" type="text" optional="true" label="Specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program" help="Alternatively, one can specify a comma-separated list of base models. For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations."> - <sanitizer> - <valid initial="string.ascii_uppercase,string.punctuation" /> - </sanitizer> + <expand macro="sanitize_query" + validinitial="string.ascii_uppercase,string.punctuation" /> </param> <param argument="-msub" type="select" label="Specify either nuclear, mitochondrial, chloroplast or viral to restrict to those AA models designed for specified source." help=""> <option value="nuclear">nuclear</option> @@ -373,14 +373,12 @@ <option value="viral">viral</option> </param> <param argument="-mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" > - <sanitizer> - <valid initial="string.ascii_uppercase,string.digits,x,string.punctuation" /> - </sanitizer> + <expand macro="sanitize_query" + validinitial="string.ascii_uppercase,string.digits,x,string.punctuation" /> </param> <param argument="-mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection"> - <sanitizer> - <valid initial="string.ascii_uppercase,string.punctuation" /> - </sanitizer> + <expand macro="sanitize_query" + validinitial="string.ascii_uppercase,string.punctuation" /> </param> <param argument="-cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/> <param argument="-cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/> @@ -391,9 +389,8 @@ </param> <param argument="-mtree" type="boolean" truevalue="-mtree" falsevalue="" checked="false" label="Turn on full tree search for each model considered, to obtain more accurate result"/> <param argument="-madd" type="text" optional="true" label="Specify a comma-separated list of mixture models to additionally consider for model selection" help="For example, -madd LG4M,LG4X to additionally include these two protein mixture models."> - <sanitizer> - <valid initial="string.ascii_uppercase,string.digits,string.punctuation" /> - </sanitizer> + <expand macro="sanitize_query" + validinitial="string.ascii_uppercase,string.digits,string.punctuation" /> </param> <param argument="-mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/> </section> @@ -402,15 +399,11 @@ </section> <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity"> <param argument="-a" type="text" optional="true" label="Specify the Gamma shape parameter (default: estimate)"> - <sanitizer> - <valid initial="string.printable" /> - </sanitizer> + <expand macro="sanitize_query" /> </param> <param argument="-gmedian" type="boolean" truevalue="-gmedian" falsevalue="" checked="false" label="Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994)"/> <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)"> - <sanitizer> - <valid initial="string.printable" /> - </sanitizer> + <expand macro="sanitize_query" /> </param> <param argument="--opt_gamma_inv" type="boolean" truevalue="--opt-gamma-inv" falsevalue="" checked="false" label="Perform more thorough estimation for +I+G model parameters"/> <param argument="-wsr" type="boolean" truevalue="-wsr" falsevalue="" checked="false" label="Write per-site rates to .rate file"/> @@ -500,9 +493,8 @@ </section> <section name="miscellaneous_options" expanded="False" title="Miscellaneous options"> <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment."> - <sanitizer> - <valid initial="string.digits,string.punctuation" /> - </sanitizer> + <expand macro="sanitize_query" + validinitial="string.digits,string.punctuation" /> </param> </section> </inputs> @@ -641,7 +633,7 @@ </output> </test> </tests> - <help> + <help><![CDATA[ IQ-TREE ======= @@ -922,7 +914,7 @@ From this figure, the branching patterns within reptiles are poorly supported (e.g. **Sphenodon** with SH-aLRT: 39%, UFBoot: 51% and **Turtle** with SH-aLRT: 85%, UFBoot: 72%) as well as the phylogenetic position of **Seal** within mammals (SH-aLRT: 68.3%, UFBoot: 75%). Other branches appear to be well supported. - </help> + ]]></help> <citations> <citation type="doi">10.1093/molbev/msu300</citation> <citation type="doi">10.1093/molbev/mst024</citation> |
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| diff -r 288db50d1fb9 -r d1c340a5664b iqtree_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/iqtree_macros.xml Wed Oct 17 11:43:10 2018 -0400 |
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| @@ -0,0 +1,20 @@ +<macros> + <token name="@TOOL_VERSION@">1.5.5</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">iqtree</requirement> + </requirements> + </xml> + + <xml name="sanitize_query" token_validinitial="string.printable"> + <sanitizer> + <valid initial="@VALIDINITIAL@"> + <remove value="'" /> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'" /> + </mapping> + </sanitizer> + </xml> +</macros> |