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comparison clearcut.xml @ 0:f979130469f4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:48:09 -0400
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children 5c368b76eff7
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-1:000000000000 0:f979130469f4
1 <tool profile="16.07" id="mothur_clearcut" name="Clearcut" version="@WRAPPER_VERSION@.0">
2 <description>Generate a tree using relaxed neighbor joining</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$input.infile" input.infile.dat &&
14
15 echo 'clearcut(
16 #if $input.source == "dna":
17 fasta=input.infile.dat,
18 DNA=true,
19 #elif $input.source == "aa":
20 fasta=input.infile.dat,
21 protein=true,
22 #elif $input.source == "phylip":
23 phylip=input.infile.dat,
24 #end if
25 #if $matrixout == "true":
26 matrixout=matrixout.dist,
27 #end if
28 #if $seed:
29 seed=$seed,
30 #end if
31 ntrees=$ntrees,
32 norandom=$norandom,
33 shuffle=$shuffle,
34 expblen=$expblen,
35 expdist=$expdist,
36 neighbor=$neighbor
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 | tee mothur.out.log
41 ]]></command>
42 <inputs>
43 <conditional name="input">
44 <param name="source" type="select" label="Distance Matrix">
45 <option value="dna">DNA Alignment Fasta</option>
46 <option value="aa">Protein Alignment Fasta</option>
47 <option value="phylip">Phylip Distance Matrix</option>
48 </param>
49 <when value="dna">
50 <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
51 </when>
52 <when value="aa">
53 <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
54 </when>
55 <when value="phylip">
56 <param name="infile" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
57 </when>
58 </conditional>
59 <param name="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/>
60 <param name="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (default 1)"/>
61 <param name="norandom" type="boolean" checked="false" truevalue="true" falsevalue="false" label="norandom - Attempt joins deterministically"/>
62 <param name="shuffle" type="boolean" checked="false" truevalue="true" falsevalue="false" label="shuffle - Randomly shuffle the distance matrix"/>
63 <param name="neighbor" type="boolean" checked="true" truevalue="true" falsevalue="false" label="neighbor - Use traditional Neighbor-Joining algorithm"/>
64 <param name="expblen" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expblen - Use exponential notation for branch lengths"/>
65 <param name="expdist" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expdist - Use exponential notation for distance"/>
66 <param name="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="false" label="matrixout - Generate a Distance Matrix"/>
67 </inputs>
68 <outputs>
69 <expand macro="logfile-output"/>
70 <data name="tree" format="tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/>
71 <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix">
72 <filter>matrixout</filter>
73 </data>
74 </outputs>
75 <tests>
76 <test><!-- test with phylip and default params-->
77 <param name="source" value="phylip"/>
78 <param name="infile" value="env.dist"/>
79 <output name="tree" md5="9c78d54267a985c8ae37dcfbddf6f8d0"/>
80 <expand macro="logfile-test"/>
81 </test>
82 <test><!-- test with phylip and params set-->
83 <param name="source" value="phylip"/>
84 <param name="infile" value="env.dist"/>
85 <param name="ntrees" value="3"/>
86 <param name="shuffle" value="true"/>
87 <param name="norandom" value="true"/>
88 <param name="neighbor" value="false"/>
89 <param name="expblen" value="ON"/>
90 <param name="expdist" value="ON"/>
91 <param name="matrixout" value="true"/>
92 <output name="tree" >
93 <assert_contents>
94 <has_text text="group"/>
95 </assert_contents>
96 </output>
97 <output name="matrix" md5="ebc0c296d46cbe4b8d50780b9f5f8314" ftype="mothur.lower.dist"/>
98 <expand macro="logfile-test"/>
99 </test>
100 <test><!-- test with fasta (dna) and matrixout-->
101 <param name="source" value="dna"/>
102 <param name="infile" value="amazon.align_head"/>
103 <param name="matrixout" value="true"/>
104 <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/>
105 <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/>
106 <expand macro="logfile-test"/>
107 </test>
108 </tests>
109 <help>
110 <![CDATA[
111
112 @MOTHUR_OVERVIEW@
113
114 **Command Documentation**
115
116 The clearcut_ command runs clearcut
117
118 The clearcut command allows mothur users to run the clearcut_program_ from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/
119
120 Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ).
121
122 Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input. If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura). Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix.
123
124 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/
125 .. _clearcut: https://www.mothur.org/wiki/Clearcut
126
127 v.1.20.0: Trivial upgrade to Mothur 1.33
128 ]]>
129 </help>
130 <expand macro="citations"/>
131 </tool>