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comparison fasttree.xml @ 3:3aa7c6da1696 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree commit 54cc70552f8891ab5db124e9e640247e1545b937
author iuc
date Sat, 05 Oct 2024 10:02:39 +0000
parents e005e659ae21
children bc939965ce41
comparison
equal deleted inserted replaced
2:e005e659ae21 3:3aa7c6da1696
1 <?xml version="1.0"?> 1 <tool id="fasttree" name="FASTTREE" version="@VERSION@+galaxy3" profile="23.1">
2 <tool id="fasttree" name="FASTTREE" version="@VERSION@+galaxy1" profile="18.01">
3 <description>build maximum-likelihood phylogenetic trees</description> 2 <description>build maximum-likelihood phylogenetic trees</description>
4 <macros> 3 <macros>
5 <token name="@VERSION@">2.1.10</token> 4 <token name="@VERSION@">2.1.10</token>
6 </macros> 5 </macros>
6 <xrefs>
7 <xref type="bio.tools">fasttree</xref>
8 </xrefs>
7 <requirements> 9 <requirements>
8 <requirement type="package" version="@VERSION@">fasttree</requirement> 10 <requirement type="package" version="@VERSION@">fasttree</requirement>
9 </requirements> 11 </requirements>
10 <version_command>FastTree</version_command> 12 <version_command><![CDATA[FastTree 2>&1 >/dev/null | head -n 1 | cut -d" " -f 5]]></version_command>
11 <command detect_errors="aggressive"> 13 <command detect_errors="aggressive">
12 <![CDATA[ 14 <![CDATA[
13 FastTree 15 FastTree
14 16
15 $model_selector.format 17 $model_selector.format
43 < '$input' > '$output' 45 < '$input' > '$output'
44 46
45 #if $save_logfile: 47 #if $save_logfile:
46 2> '$log' 48 2> '$log'
47 #end if 49 #end if
48
49 ]]> 50 ]]>
50 </command> 51 </command>
51 <inputs> 52 <inputs>
52 <conditional name="input_selector"> 53 <conditional name="input_selector">
53 <param name="select_format" type="select" label="Aligned sequences file (FASTA or Phylip format)"> 54 <param name="select_format" type="select" label="Aligned sequences file (FASTA or Phylip format)">
54 <option value="fasta" selected="true">fasta</option> 55 <option value="fasta" selected="true">fasta</option>
55 <option value="phylip">phylip</option> 56 <option value="phylip">phylip</option>
56 </param> 57 </param>
57 <when value="fasta"> 58 <when value="fasta">
58 <param format="fasta" name="input" type="data" multiple="false" label="FASTA file"/> 59 <param format="fasta" name="input" type="data" multiple="false" label="FASTA file"/>
59 <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." /> 60 <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." />
60 <conditional name="intree_selector"> 61 <conditional name="intree_selector">
61 <param name="intree_format" type="select" label="Set starting tree(s)"> 62 <param name="intree_format" type="select" label="Set starting tree(s)">
62 <option value="none" selected="true">No starting trees</option> 63 <option value="none" selected="true">No starting trees</option>
63 <option value="one">Use starting tree</option> 64 <option value="one">Use starting tree</option>
64 </param> 65 </param>
129 </when> 130 </when>
130 </conditional> 131 </conditional>
131 <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." /> 132 <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." />
132 <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."/> 133 <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."/>
133 <param name="likelihood" argument="-noml" type="boolean" truevalue="-noml" falsevalue="" checked="false" label = "Turn off maximum-likelihood." /> 134 <param name="likelihood" argument="-noml" type="boolean" truevalue="-noml" falsevalue="" checked="false" label = "Turn off maximum-likelihood." />
134 <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)" /> 135 <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)" />
135 <param name="pseudo" argument="-pseudo" type="boolean" truevalue="-pseudo" falsevalue="" checked="false" label="Use pseudocounts" help="Recommended for highly gapped/fragmentary sequences." /> 136 <param argument="-pseudo" type="boolean" truevalue="-pseudo" falsevalue="" checked="false" label="Use pseudocounts" help="Recommended for highly gapped/fragmentary sequences." />
136 <param name="mllen" argument="-mllen" type="boolean" truevalue="-mllen" falsevalue="" checked="false" label="Optimize branch lengths without ML NNIs." /> 137 <param argument="-mllen" type="boolean" truevalue="-mllen" falsevalue="" checked="false" label="Optimize branch lengths without ML NNIs." />
137 </when> 138 </when>
138 </conditional> 139 </conditional>
139 </inputs> 140 </inputs>
140 <outputs> 141 <outputs>
141 <data name="output" format="nhx" label="${tool.name} on ${on_string}:tree.nhx" /> 142 <data name="output" format="nhx" label="${tool.name} on ${on_string}:tree.nhx" />
142 <data name="log" format="txt" label="${tool.name} on ${on_string}:log_FastTree_run.txt"> 143 <data name="log" format="txt" label="${tool.name} on ${on_string}:log_FastTree_run.txt">
143 <filter>save_logfile</filter> 144 <filter>save_logfile</filter>
144 </data> 145 </data>
145 </outputs> 146 </outputs>
146 <tests> 147 <tests>
147 <test> 148 <test expect_num_outputs="2">
148 <param name="select_format" value="fasta" /> 149 <param name="select_format" value="fasta" />
149 <param name="model" value="" /> 150 <param name="model" value="" />
150 <param name="input" value="aligned.fasta" /> 151 <param name="input" value="aligned.fasta" />
151 <param name="format" value="-nt" /> 152 <param name="format" value="-nt" />
152 <param name="save_logfile" value="true" /> 153 <param name="save_logfile" value="true" />