Mercurial > repos > iuc > mothur_remove_otulabels
comparison remove.otulabels.xml @ 2:a8863051d303 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:22:34 -0400 |
parents | afd434bb48af |
children | 5133ef623148 |
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1:08579dd3bf72 | 2:a8863051d303 |
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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 'remove.otulabels( | 16 echo 'remove.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.data, | 18 constaxonomy=infile.otu.data, |
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 $infile.label: |
33 label=${ str($infile.label).replace(",","-") }, | 33 label=${ str($infile.label).replace(",","-") }, |
34 #end if | 34 #end if |
35 accnos=accnos.dat | 35 accnos=accnos.dat |
36 )' | 36 )' |
37 | sed 's/ //g' ## mothur trips over whitespace | 37 | sed 's/ //g' ## mothur trips over whitespace |
38 | mothur | 38 | mothur |
39 | tee mothur.out.log | 39 | tee mothur.out.log |
40 ]]></command> | 40 ]]></command> |
41 <inputs> | 41 <inputs> |
42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/> | 42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/> |
43 <conditional name="infile"> | 43 <conditional name="infile"> |
44 <param name="intype" type="select" label="Which type of files will you be supplying?" help=""> | 44 <param name="intype" type="select" label="Which type of files will you be supplying?" help=""> |
53 </when> | 53 </when> |
54 <when value="in_other"> | 54 <when value="in_other"> |
55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/> | 55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/> |
56 </when> | 56 </when> |
57 </conditional> | 57 </conditional> |
58 <expand macro="param-savelog"/> | |
58 </inputs> | 59 </inputs> |
59 <outputs> | 60 <outputs> |
60 <expand macro="logfile-output"/> | 61 <expand macro="logfile-output"/> |
61 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${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> |
64 <test><!-- test with shared/list input and label selection --> | 65 <test><!-- test with shared/list input and label selection --> |
65 <param name="accnos" value="amazon.accnos.otulabels"/> | 66 <param name="accnos" value="amazon.accnos.otulabels"/> |
66 <param name="intype" value="in_shared"/> | 67 <param name="intype" value="in_shared"/> |
67 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> | 68 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> |
68 <param name="label" value="0.22"/> | 69 <param name="label" value="0.22"/> |
69 <output name="pick_out" md5="8ab2a6afd9a2547e3c4ffe2e83375c33" ftype="mothur.list"/> | 70 <output name="pick_out" ftype="mothur.list"> |
71 <assert_contents> | |
72 <expand macro="test-list-format"/> | |
73 <has_text text="U68686"/> | |
74 <has_text text="0.22"/> | |
75 <not_has_text text="0.03"/> | |
76 </assert_contents> | |
77 </output> | |
78 <param name="savelog" value="true"/> | |
70 <expand macro="logfile-test"/> | 79 <expand macro="logfile-test"/> |
71 </test> | 80 </test> |
72 <test><!-- test with constaxonomy/otucorr/corraxes file --> | 81 <test><!-- test with constaxonomy/otucorr/corraxes file --> |
73 <param name="accnos" value="amazon.accnos.otulabels"/> | 82 <param name="accnos" value="amazon.accnos.otulabels"/> |
74 <param name="intype" value="in_other"/> | 83 <param name="intype" value="in_other"/> |
75 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/> | 84 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/> |
76 <output name="pick_out" md5="9bffef40bf6e879737835cf7323c5ce4" ftype="mothur.axes"/> | 85 <output name="pick_out" ftype="mothur.axes"> |
86 <assert_contents> | |
87 <expand macro="test-axes-format"/> | |
88 <has_text text="U68686"/> | |
89 </assert_contents> | |
90 </output> | |
91 <param name="savelog" value="true"/> | |
77 <expand macro="logfile-test"/> | 92 <expand macro="logfile-test"/> |
78 </test> | 93 </test> |
79 </tests> | 94 </tests> |
80 <help> | 95 <help><![CDATA[ |
81 <![CDATA[ | |
82 | 96 |
83 @MOTHUR_OVERVIEW@ | 97 @MOTHUR_OVERVIEW@ |
84 | 98 |
85 **Command Documentation** | 99 **Command Documentation** |
86 | 100 |
88 | 102 |
89 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu | 103 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu |
90 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes | 104 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes |
91 .. _otu.association: https://www.mothur.org/wiki/Otu.association | 105 .. _otu.association: https://www.mothur.org/wiki/Otu.association |
92 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels | 106 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels |
93 ]]> | 107 |
94 </help> | 108 ]]></help> |
95 <expand macro="citations"/> | 109 <expand macro="citations"/> |
96 </tool> | 110 </tool> |