Mercurial > repos > iuc > mothur_clearcut
comparison clearcut.xml @ 3:959bd3b9fa75 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:07:05 -0400 |
| parents | 5c368b76eff7 |
| children | 20e764494303 |
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| 2:5c368b76eff7 | 3:959bd3b9fa75 |
|---|---|
| 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 <expand macro="param-savelog"/> | |
| 67 </inputs> | 68 </inputs> |
| 68 <outputs> | 69 <outputs> |
| 69 <expand macro="logfile-output"/> | 70 <expand macro="logfile-output"/> |
| 70 <data name="tree" format="mothur.tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/> | 71 <data name="tree" format="mothur.tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/> |
| 71 <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix"> | 72 <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix"> |
| 75 <tests> | 76 <tests> |
| 76 <test><!-- test with phylip and default params--> | 77 <test><!-- test with phylip and default params--> |
| 77 <param name="source" value="phylip"/> | 78 <param name="source" value="phylip"/> |
| 78 <param name="infile" value="env.dist"/> | 79 <param name="infile" value="env.dist"/> |
| 79 <output name="tree" md5="9c78d54267a985c8ae37dcfbddf6f8d0"/> | 80 <output name="tree" md5="9c78d54267a985c8ae37dcfbddf6f8d0"/> |
| 81 <param name="savelog" value="true"/> | |
| 80 <expand macro="logfile-test"/> | 82 <expand macro="logfile-test"/> |
| 81 </test> | 83 </test> |
| 82 <test><!-- test with phylip and params set--> | 84 <test><!-- test with phylip and params set--> |
| 83 <param name="source" value="phylip"/> | 85 <param name="source" value="phylip"/> |
| 84 <param name="infile" value="env.dist"/> | 86 <param name="infile" value="env.dist"/> |
| 93 <assert_contents> | 95 <assert_contents> |
| 94 <has_text text="group"/> | 96 <has_text text="group"/> |
| 95 </assert_contents> | 97 </assert_contents> |
| 96 </output> | 98 </output> |
| 97 <output name="matrix" md5="ebc0c296d46cbe4b8d50780b9f5f8314" ftype="mothur.lower.dist"/> | 99 <output name="matrix" md5="ebc0c296d46cbe4b8d50780b9f5f8314" ftype="mothur.lower.dist"/> |
| 100 <param name="savelog" value="true"/> | |
| 98 <expand macro="logfile-test"/> | 101 <expand macro="logfile-test"/> |
| 99 </test> | 102 </test> |
| 100 <test><!-- test with fasta (dna) and matrixout--> | 103 <test><!-- test with fasta (dna) and matrixout--> |
| 101 <param name="source" value="dna"/> | 104 <param name="source" value="dna"/> |
| 102 <param name="infile" value="amazon.align_head"/> | 105 <param name="infile" value="amazon.align_head"/> |
| 103 <param name="matrixout" value="true"/> | 106 <param name="matrixout" value="true"/> |
| 104 <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/> | 107 <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/> |
| 105 <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/> | 108 <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/> |
| 109 <param name="savelog" value="true"/> | |
| 106 <expand macro="logfile-test"/> | 110 <expand macro="logfile-test"/> |
| 107 </test> | 111 </test> |
| 108 </tests> | 112 </tests> |
| 109 <help> | 113 <help><![CDATA[ |
| 110 <![CDATA[ | |
| 111 | 114 |
| 112 @MOTHUR_OVERVIEW@ | 115 @MOTHUR_OVERVIEW@ |
| 113 | 116 |
| 114 **Command Documentation** | 117 **Command Documentation** |
| 115 | 118 |
| 123 | 126 |
| 124 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/ | 127 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/ |
| 125 .. _clearcut: https://www.mothur.org/wiki/Clearcut | 128 .. _clearcut: https://www.mothur.org/wiki/Clearcut |
| 126 | 129 |
| 127 v.1.20.0: Trivial upgrade to Mothur 1.33 | 130 v.1.20.0: Trivial upgrade to Mothur 1.33 |
| 128 ]]> | 131 |
| 129 </help> | 132 ]]></help> |
| 130 <expand macro="citations"/> | 133 <expand macro="citations"/> |
| 131 </tool> | 134 </tool> |