Mercurial > repos > iuc > mothur_sub_sample

comparison sub.sample.xml @ 3:1f5904c5ee42 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 10:11:07 -0500
parents f18e9f139d14
children 90c49ac0776e
comparison
equal deleted inserted replaced
2:e04f78ea3e59 3:1f5904c5ee42
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 "$input.otu" input_otu.dat && 13 ln -s '$input.otu' input_otu.dat &&
14 ln -s "$count" count.dat && 14 ln -s '$count' count.dat &&
15 ln -s "$taxonomy" taxonomy.dat && 15 ln -s '$taxonomy' taxonomy.dat &&
16 #if $input.format == "fasta": 16 #if $input.format == "fasta":
17 ln -s "$input.name_in" input_name_in.dat && 17 ln -s '$input.name_in' input_name_in.dat &&
18 #end if
19 #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes":
20 ln -s '$input.use_group.group_in' input_use_group_group_in.dat &&
21 #end if
22
23 echo 'sub.sample(
24 #if $input.format == "fasta":
25 fasta=input_otu.dat
26 #if $input.name_in:
27 ,name=input_name_in.dat
18 #end if 28 #end if
19 #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes": 29 #else
20 ln -s "$input.use_group.group_in" input_use_group_group_in.dat && 30 #if $input.format == "list":
31 list=input_otu.dat
32 #elif $input.format == "sabund":
33 sabund=input_otu.dat
34 #elif $input.format == "rabund":
35 rabund=input_otu.dat
36 #elif $input.format == "shared":
37 shared=input_otu.dat
38 #if $input.groups:
39 ,groups=${ str($input.groups).replace(",","-") }
40 #end if
21 #end if 41 #end if
22 42 #if $input.label:
23 echo 'sub.sample( 43 ,label=${ str($input.label).replace(",","-") }
24 #if $input.format == "fasta": 44 #end if
25 fasta=input_otu.dat 45 #end if
26 #if $input.name_in: 46 #if $input.format == "fasta" or $input.format == "list":
27 ,name=input_name_in.dat 47 #if $input.use_group.to_filter == "yes":
28 #end if 48 ,group=input_use_group_group_in.dat
29 #else 49 #if $input.use_group.groups:
30 #if $input.format == "list": 50 ,groups=${ str($input.use_group.groups).replace(",","-") }
31 list=input_otu.dat
32 #elif $input.format == "sabund":
33 sabund=input_otu.dat
34 #elif $input.format == "rabund":
35 rabund=input_otu.dat
36 #elif $input.format == "shared":
37 shared=input_otu.dat
38 #if $input.groups:
39 ,groups=${ str($input.groups).replace(",","-") }
40 #end if
41 #end if
42 #if $input.label:
43 ,label=${ str($input.label).replace(",","-") }
44 #end if
45 #end if 51 #end if
46 #if $input.format == "fasta" or $input.format == "list": 52 ,persample=$input.use_group.persample
47 #if $input.use_group.to_filter == "yes": 53 #end if
48 ,group=input_use_group_group_in.dat 54 #end if
49 #if $input.use_group.groups: 55 #if $count:
50 ,groups=${ str($input.use_group.groups).replace(",","-") } 56 ,count=count.dat
51 #end if 57 #end if
52 ,persample=$input.use_group.persample 58 #if $taxonomy:
53 #end if 59 ,taxonomy=taxonomy.dat
54 #end if 60 #end if
55 #if $count: 61 #if $size:
56 ,count=count.dat 62 ,size=$size
57 #end if 63 #end if
58 #if $taxonomy: 64 )'
59 ,taxonomy=taxonomy.dat 65 | sed 's/ //g' ## mothur trips over whitespace
60 #end if 66 | mothur
61 #if $size: 67 | tee mothur.out.log
62 ,size=$size
63 #end if
64 )'
65 | sed 's/ //g' ## mothur trips over whitespace
66 | mothur
67 | tee mothur.out.log
68 ]]></command> 68 ]]></command>
69 <inputs> 69 <inputs>
70 <conditional name="input"> 70 <conditional name="input">
71 <param name="format" type="select" label="Select type of data to sub sample"> 71 <param name="format" type="select" label="Select type of data to sub sample">
72 <option value="fasta">FASTA</option> 72 <option value="fasta">FASTA</option>
283 </assert_contents> 283 </assert_contents>
284 </output> 284 </output>
285 <expand macro="logfile-test"/> 285 <expand macro="logfile-test"/>
286 </test> 286 </test>
287 </tests> 287 </tests>
288 <help> 288 <help><![CDATA[
289 <![CDATA[
290 289
291 @MOTHUR_OVERVIEW@ 290 @MOTHUR_OVERVIEW@
292 291
293 **Command Documentation** 292 **Command Documentation**
294 293
298 .. _shared: https://www.mothur.org/wiki/Shared_file 297 .. _shared: https://www.mothur.org/wiki/Shared_file
299 .. _rabund: https://www.mothur.org/wiki/Rabund_file 298 .. _rabund: https://www.mothur.org/wiki/Rabund_file
300 .. _sabund: https://www.mothur.org/wiki/Sabund_file 299 .. _sabund: https://www.mothur.org/wiki/Sabund_file
301 .. _sub.sample: https://www.mothur.org/wiki/Sub.sample 300 .. _sub.sample: https://www.mothur.org/wiki/Sub.sample
302 301
303 ]]> 302 ]]></help>
304 </help>
305 <expand macro="citations"/> 303 <expand macro="citations"/>
306 </tool> 304 </tool>