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comparison clearcut.xml @ 4:0cbf1a5ba59c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:16:25 -0500
parents 6fb0ea14dac3
children f872e70bdeef
comparison
equal deleted inserted replaced
3:6fb0ea14dac3 4:0cbf1a5ba59c
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$input.infile" input.infile.dat && 13 ln -s '$input.infile' input.infile.dat &&
14 14
15 echo 'clearcut( 15 echo 'clearcut(
16 #if $input.source == "dna": 16 #if $input.source == "dna":
17 fasta=input.infile.dat, 17 fasta=input.infile.dat,
18 DNA=true, 18 DNA=true,
19 #elif $input.source == "aa": 19 #elif $input.source == "aa":
20 fasta=input.infile.dat, 20 fasta=input.infile.dat,
21 protein=true, 21 protein=true,
22 #elif $input.source == "phylip": 22 #elif $input.source == "phylip":
23 phylip=input.infile.dat, 23 phylip=input.infile.dat,
24 #end if 24 #end if
25 #if $matrixout == "true": 25 #if $matrixout == "true":
26 matrixout=matrixout.dist, 26 matrixout=matrixout.dist,
27 #end if 27 #end if
28 #if $seed: 28 #if $seed:
29 seed=$seed, 29 seed=$seed,
30 #end if 30 #end if
31 ntrees=$ntrees, 31 ntrees=$ntrees,
32 norandom=$norandom, 32 norandom=$norandom,
33 shuffle=$shuffle, 33 shuffle=$shuffle,
34 expblen=$expblen, 34 expblen=$expblen,
35 expdist=$expdist, 35 expdist=$expdist,
36 neighbor=$neighbor 36 neighbor=$neighbor
37 )' 37 )'
38 | sed 's/ //g' ## mothur trips over whitespace 38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 39 | mothur
40 | tee mothur.out.log 40 | tee mothur.out.log
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <conditional name="input"> 43 <conditional name="input">
44 <param name="source" type="select" label="Distance Matrix"> 44 <param name="source" type="select" label="Distance Matrix">
45 <option value="dna">DNA Alignment Fasta</option> 45 <option value="dna">DNA Alignment Fasta</option>
46 <option value="aa">Protein Alignment Fasta</option> 46 <option value="aa">Protein Alignment Fasta</option>
47 <option value="phylip">Phylip Distance Matrix</option> 47 <option value="phylip">Phylip Distance Matrix</option>
48 </param> 48 </param>
49 <when value="dna"> 49 <when value="dna">
50 <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> 50 <param argument="fasta" name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
51 </when> 51 </when>
52 <when value="aa"> 52 <when value="aa">
53 <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> 53 <param argument="fasta" name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
54 </when> 54 </when>
55 <when value="phylip"> 55 <when value="phylip">
56 <param name="infile" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 56 <param argument="phylip" name="infile" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
57 </when> 57 </when>
58 </conditional> 58 </conditional>
59 <param name="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/> 59 <param argument="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)"/> 60 <param argument="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"/> 61 <param argument="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"/> 62 <param argument="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"/> 63 <param argument="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"/> 64 <param argument="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"/> 65 <param argument="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"/> 66 <param argument="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="false" label="matrixout - Generate a Distance Matrix"/>
67 </inputs> 67 </inputs>
68 <outputs> 68 <outputs>
69 <expand macro="logfile-output"/> 69 <expand macro="logfile-output"/>
70 <data name="tree" format="mothur.tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/> 70 <data name="tree" format="mothur.tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/>
71 <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix"> 71 <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix">
104 <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/> 104 <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/>
105 <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/> 105 <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/>
106 <expand macro="logfile-test"/> 106 <expand macro="logfile-test"/>
107 </test> 107 </test>
108 </tests> 108 </tests>
109 <help> 109 <help><![CDATA[
110 <![CDATA[
111 110
112 @MOTHUR_OVERVIEW@ 111 @MOTHUR_OVERVIEW@
113 112
114 **Command Documentation** 113 **Command Documentation**
115 114
123 122
124 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/ 123 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/
125 .. _clearcut: https://www.mothur.org/wiki/Clearcut 124 .. _clearcut: https://www.mothur.org/wiki/Clearcut
126 125
127 v.1.20.0: Trivial upgrade to Mothur 1.33 126 v.1.20.0: Trivial upgrade to Mothur 1.33
128 ]]> 127
129 </help> 128 ]]></help>
130 <expand macro="citations"/> 129 <expand macro="citations"/>
131 </tool> 130 </tool>