Mercurial > repos > iuc > mothur_get_otulabels
comparison get.otulabels.xml @ 2:29769fb14cd2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:19:23 -0400 |
| parents | ca0c577f910d |
| children |
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| 1:56b4c4b3ce7c | 2:29769fb14cd2 |
|---|---|
| 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 "$infile.otu" infile.otu.dat && | 13 ln -s '$infile.otu' infile.otu.dat && |
| 14 ln -s "$accnos" accnos.dat && | 14 ln -s '$accnos' accnos.dat && |
| 15 | 15 |
| 16 echo 'get.otulabels( | 16 echo 'get.otulabels( |
| 17 #if $infile.otu.is_of_type("mothur.cons.taxonomy"): | 17 #if $infile.otu.is_of_type("mothur.cons.taxonomy"): |
| 18 constaxonomy=infile.otu.dat, | 18 constaxonomy=infile.otu.dat, |
| 19 #end if | 19 #end if |
| 20 #if $infile.otu.is_of_type("mothur.otu.corr"): | 20 #if $infile.otu.is_of_type("mothur.otu.corr"): |
| 21 otucorr=infile.otu.dat, | 21 otucorr=infile.otu.dat, |
| 22 #end if | 22 #end if |
| 23 #if $infile.otu.is_of_type("mothur.axes"): | 23 #if $infile.otu.is_of_type("mothur.axes"): |
| 24 corraxes=infile.otu.dat, | 24 corraxes=infile.otu.dat, |
| 25 #end if | 25 #end if |
| 26 #if $infile.otu.is_of_type("mothur.list"): | 26 #if $infile.otu.is_of_type("mothur.list"): |
| 27 list=infile.otu.dat, | 27 list=infile.otu.dat, |
| 28 #end if | 28 #end if |
| 29 #if $infile.otu.is_of_type("mothur.shared"): | 29 #if $infile.otu.is_of_type("mothur.shared"): |
| 30 shared=infile.otu.dat, | 30 shared=infile.otu.dat, |
| 31 #end if | 31 #end if |
| 32 #if $infile.intype == "in_shared" and $infile.label: | 32 #if $infile.intype == "in_shared" and $infile.label: |
| 33 label=$infile.label, | 33 label=$infile.label, |
| 34 #end if | 34 #end if |
| 35 accnos=accnos.dat | 35 accnos=accnos.dat |
| 36 )' | 36 )' |
| 37 | sed 's/ //g' ## mothur trips over whitespace | 37 | sed 's/ //g' ## mothur trips over whitespace |
| 38 | mothur | 38 | mothur |
| 39 | tee mothur.out.log | 39 | tee mothur.out.log |
| 40 ]]></command> | 40 ]]></command> |
| 41 <inputs> | 41 <inputs> |
| 42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/> | 42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/> |
| 43 <conditional name="infile"> | 43 <conditional name="infile"> |
| 44 <param name="intype" type="select" label="Which type of files will you be supplying?" help=""> | 44 <param name="intype" type="select" label="Which type of files will you be supplying?" help=""> |
| 53 </when> | 53 </when> |
| 54 <when value="in_other"> | 54 <when value="in_other"> |
| 55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/> | 55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/> |
| 56 </when> | 56 </when> |
| 57 </conditional> | 57 </conditional> |
| 58 <expand macro="param-savelog"/> | |
| 58 </inputs> | 59 </inputs> |
| 59 <outputs> | 60 <outputs> |
| 60 <expand macro="logfile-output"/> | 61 <expand macro="logfile-output"/> |
| 61 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/> | 62 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/> |
| 62 </outputs> | 63 </outputs> |
| 65 <param name="intype" value="in_shared"/> | 66 <param name="intype" value="in_shared"/> |
| 66 <param name="accnos" value="amazon.accnos.otulabels"/> | 67 <param name="accnos" value="amazon.accnos.otulabels"/> |
| 67 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | 68 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
| 68 <param name="label" value="0.22"/> | 69 <param name="label" value="0.22"/> |
| 69 <output name="pick_out" md5="1868b58c69f48fe0ae14113d1fc50b33" ftype="mothur.shared"/> | 70 <output name="pick_out" md5="1868b58c69f48fe0ae14113d1fc50b33" ftype="mothur.shared"/> |
| 71 <param name="savelog" value="true"/> | |
| 70 <expand macro="logfile-test"/> | 72 <expand macro="logfile-test"/> |
| 71 </test> | 73 </test> |
| 72 <test> | 74 <test> |
| 73 <param name="intype" value="in_other"/> | 75 <param name="intype" value="in_other"/> |
| 74 <param name="accnos" value="amazon.accnos.otulabels"/> | 76 <param name="accnos" value="amazon.accnos.otulabels"/> |
| 75 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/> | 77 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/> |
| 76 <output name="pick_out" md5="c5f9d1a80b85cce640f25eb89cb67509" ftype="mothur.axes"/> | 78 <output name="pick_out" md5="c5f9d1a80b85cce640f25eb89cb67509" ftype="mothur.axes"/> |
| 79 <param name="savelog" value="true"/> | |
| 77 <expand macro="logfile-test"/> | 80 <expand macro="logfile-test"/> |
| 78 </test> | 81 </test> |
| 79 </tests> | 82 </tests> |
| 80 <help> | 83 <help><![CDATA[ |
| 81 <![CDATA[ | |
| 82 | 84 |
| 83 @MOTHUR_OVERVIEW@ | 85 @MOTHUR_OVERVIEW@ |
| 84 | 86 |
| 85 | 87 |
| 86 **Command Documentation** | 88 **Command Documentation** |
| 87 | 89 |
| 88 The get.otulabels_ command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. | 90 The get.otulabels command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. |
| 89 | 91 |
| 90 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu | 92 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu |
| 91 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes | 93 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes |
| 92 .. _otu.association: https://www.mothur.org/wiki/Otu.association | 94 .. _otu.association: https://www.mothur.org/wiki/Otu.association |
| 93 | 95 |
| 94 v.1.27.0: Added list and shared parameters, updated to Mothur 1.33 | 96 v.1.27.0: Added list and shared parameters, updated to Mothur 1.33 |
| 95 ]]> | 97 |
| 96 </help> | 98 ]]></help> |
| 97 <expand macro="citations"/> | 99 <expand macro="citations"/> |
| 98 </tool> | 100 </tool> |