| Previous changeset 2:e005e659ae21 (2020-02-20) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937 |
|
modified:
fasttree.xml |
| b |
| diff -r e005e659ae21 -r 3aa7c6da1696 fasttree.xml --- a/fasttree.xml Thu Feb 20 14:51:32 2020 -0500 +++ b/fasttree.xml Sat Oct 05 10:02:39 2024 +0000 |
| [ |
| @@ -1,13 +1,15 @@ -<?xml version="1.0"?> -<tool id="fasttree" name="FASTTREE" version="@VERSION@+galaxy1" profile="18.01"> +<tool id="fasttree" name="FASTTREE" version="@VERSION@+galaxy3" profile="23.1"> <description>build maximum-likelihood phylogenetic trees</description> <macros> <token name="@VERSION@">2.1.10</token> </macros> + <xrefs> + <xref type="bio.tools">fasttree</xref> + </xrefs> <requirements> <requirement type="package" version="@VERSION@">fasttree</requirement> </requirements> - <version_command>FastTree</version_command> + <version_command><![CDATA[FastTree 2>&1 >/dev/null | head -n 1 | cut -d" " -f 5]]></version_command> <command detect_errors="aggressive"> <![CDATA[ FastTree @@ -45,7 +47,6 @@ #if $save_logfile: 2> '$log' #end if - ]]> </command> <inputs> @@ -56,7 +57,7 @@ </param> <when value="fasta"> <param format="fasta" name="input" type="data" multiple="false" label="FASTA file"/> - <param name="quote" argument="-quote" type="boolean" truevalue="-quote" falsevalue="" checked="false" label="Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree." help="This tool is only available for fasta input only; FastTree will not be able to read these trees back in." /> + <param argument="-quote" type="boolean" truevalue="-quote" falsevalue="" checked="false" label="Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree." help="This tool is only available for fasta input only; FastTree will not be able to read these trees back in." /> <conditional name="intree_selector"> <param name="intree_format" type="select" label="Set starting tree(s)"> <option value="none" selected="true">No starting trees</option> @@ -131,9 +132,9 @@ <param value="gamma" argument="-gamma" type="boolean" truevalue="-gamma" falsevalue="" checked="false" label="Use Gamma20" help="After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood." /> <param value="nosupport" argument="-nosupport" type="boolean" truevalue="-nosupport" falsevalue="" checked="false" label="Eliminates the support value computation. Support value computation is not recommended for wide alignments."/> <param name="likelihood" argument="-noml" type="boolean" truevalue="-noml" falsevalue="" checked="false" label = "Turn off maximum-likelihood." /> - <param name="fastest" argument="-fastest" type="boolean" truevalue="-fastest" falsevalue="" checked="false" label="Speed up the neighbor joining phase and reduce memory usage (recommended for >50,000 sequences)" /> - <param name="pseudo" argument="-pseudo" type="boolean" truevalue="-pseudo" falsevalue="" checked="false" label="Use pseudocounts" help="Recommended for highly gapped/fragmentary sequences." /> - <param name="mllen" argument="-mllen" type="boolean" truevalue="-mllen" falsevalue="" checked="false" label="Optimize branch lengths without ML NNIs." /> + <param argument="-fastest" type="boolean" truevalue="-fastest" falsevalue="" checked="false" label="Speed up the neighbor joining phase and reduce memory usage (recommended for >50,000 sequences)" /> + <param argument="-pseudo" type="boolean" truevalue="-pseudo" falsevalue="" checked="false" label="Use pseudocounts" help="Recommended for highly gapped/fragmentary sequences." /> + <param argument="-mllen" type="boolean" truevalue="-mllen" falsevalue="" checked="false" label="Optimize branch lengths without ML NNIs." /> </when> </conditional> </inputs> @@ -144,7 +145,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="2"> <param name="select_format" value="fasta" /> <param name="model" value="" /> <param name="input" value="aligned.fasta" /> |