Mercurial > repos > iuc > mothur_remove_lineage

comparison remove.lineage.xml @ 3:702f118f52f9 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 09:25:48 -0500
parents b4939bc52ca7
children 3a7f96ed57ff
comparison
equal deleted inserted replaced
2:f4b594d46586 3:702f118f52f9
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 #import re 12 #import re
13 ## create symlinks to input datasets 13 ## create symlinks to input datasets
14 ln -s "$file.taxonomy" file.taxonomy.dat && 14 ln -s '$file.taxonomy' file.taxonomy.dat &&
15 #if $file.filetype == "useconstaxonomy": 15 #if $file.filetype == "useconstaxonomy":
16 ln -s "$file.shared" file.shared.dat && 16 ln -s '$file.shared' file.shared.dat &&
17 ln -s "$file.list" file.list.dat && 17 ln -s '$file.list' file.list.dat &&
18 #end if
19 ln -s '$fasta_in' fasta_in.dat &&
20 ln -s '$group_in' group_in.dat &&
21 ln -s '$alignreport_in' alignreport_in.dat &&
22 ln -s '$list_in' list_in.dat &&
23 ln -s '$name_in' name_in.dat &&
24 ln -s '$count' count.dat &&
25
26 echo 'remove.lineage(
27 #if $file.filetype == "usetaxonomy":
28 taxonomy=file.taxonomy.dat
29 #else
30 constaxonomy=file.taxonomy.dat
31 #if $file.shared:
32 ,shared=file.shared.dat
18 #end if 33 #end if
19 ln -s "$fasta_in" fasta_in.dat && 34 #if $file.list:
20 ln -s "$group_in" group_in.dat && 35 ,list=file.list.dat
21 ln -s "$alignreport_in" alignreport_in.dat && 36 #end if
22 ln -s "$list_in" list_in.dat && 37 #end if
23 ln -s "$name_in" name_in.dat && 38 #if $file.taxons:
24 ln -s "$count" count.dat && 39 #set taxonstring=str($file.taxons).replace(",","-")
25 40 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"'
26 echo 'remove.lineage( 41 #elif $taxon:
27 #if $file.filetype == "usetaxonomy": 42 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"'
28 taxonomy=file.taxonomy.dat 43 #end if
29 #else 44 #if $fasta_in:
30 constaxonomy=file.taxonomy.dat 45 ,fasta=fasta_in.dat
31 #if $file.shared: 46 #end if
32 ,shared=file.shared.dat 47 #if $group_in:
33 #end if 48 ,group=group_in.dat
34 #if $file.list: 49 #end if
35 ,list=file.list.dat 50 #if $alignreport_in:
36 #end if 51 ,alignreport=alignreport_in.dat
37 #end if 52 #end if
38 #if $file.taxons: 53 #if $list_in:
39 #set taxonstring=str($file.taxons).replace(",","-") 54 ,list=list_in.dat
40 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"' 55 #end if
41 #elif $taxon: 56 #if $name_in:
42 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"' 57 ,name=name_in.dat
43 #end if 58 ,dups=$dups
44 #if $fasta_in: 59 #end if
45 ,fasta=fasta_in.dat 60 #if $count:
46 #end if 61 ,count=count.dat
47 #if $group_in: 62 #end if
48 ,group=group_in.dat 63 )'
49 #end if 64 | sed 's/ //g' ## mothur trips over whitespace
50 #if $alignreport_in: 65 | mothur
51 ,alignreport=alignreport_in.dat 66 | tee mothur.out.log
52 #end if
53 #if $list_in:
54 ,list=list_in.dat
55 #end if
56 #if $name_in:
57 ,name=name_in.dat
58 ,dups=$dups
59 #end if
60 #if $count:
61 ,count=count.dat
62 #end if
63 )'
64 | sed 's/ //g' ## mothur trips over whitespace
65 | mothur
66 | tee mothur.out.log
67 ]]></command> 67 ]]></command>
68 <inputs> 68 <inputs>
69 <conditional name="file"> 69 <conditional name="file">
70 <param name="filetype" type="select" label="choose which file is used"> 70 <param name="filetype" type="select" label="choose which file is used">
71 <option value="usetaxonomy" selected="true">taxonomy</option> 71 <option value="usetaxonomy" selected="true">taxonomy</option>
188 <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/> 188 <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/>
189 <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;,Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"/> 189 <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;,Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"/>
190 <output name="taxonomy_out" md5="017f53dd82f3e1afcf48778034b51685"/> 190 <output name="taxonomy_out" md5="017f53dd82f3e1afcf48778034b51685"/>
191 </test> 191 </test>
192 </tests> 192 </tests>
193 <help> 193 <help><![CDATA[
194 <![CDATA[
195 194
196 @MOTHUR_OVERVIEW@ 195 @MOTHUR_OVERVIEW@
197 196
198 **Command Documentation** 197 **Command Documentation**
199 198
204 .. _group: https://www.mothur.org/wiki/Group_file 203 .. _group: https://www.mothur.org/wiki/Group_file
205 .. _list: https://www.mothur.org/wiki/List_file 204 .. _list: https://www.mothur.org/wiki/List_file
206 .. _align.report: https://www.mothur.org/wiki/Align.seqs 205 .. _align.report: https://www.mothur.org/wiki/Align.seqs
207 .. _remove.lineage: https://www.mothur.org/wiki/Remove.lineage 206 .. _remove.lineage: https://www.mothur.org/wiki/Remove.lineage
208 207
209 ]]> 208 ]]></help>
210 </help>
211 <expand macro="citations"/> 209 <expand macro="citations"/>
212 </tool> 210 </tool>