Mercurial > repos > iuc > mothur_chimera_perseus
comparison chimera.perseus.xml @ 2:1dab91d5c40e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 22:27:06 -0400 |
parents | 35c11001da8b |
children | 128cbea05aeb |
comparison
equal
deleted
inserted
replaced
1:a23027673aba | 2:1dab91d5c40e |
---|---|
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 "$fasta" fasta.dat && | 13 ln -s '$fasta' fasta.dat && |
14 ln -s "$name" name.dat && | 14 ln -s '$name' name.dat && |
15 ln -s "$group" group.dat && | 15 ln -s '$group' group.dat && |
16 | 16 |
17 echo 'chimera.perseus( | 17 echo 'chimera.perseus( |
18 fasta=fasta.dat, | 18 fasta=fasta.dat, |
19 #if $name.is_of_type("mothur.names"): | 19 #if $name.is_of_type("mothur.names"): |
20 name=name.dat, | 20 name=name.dat, |
21 #elif $name.is_of_type("mothur.count_table"): | 21 #elif $name.is_of_type("mothur.count_table"): |
22 count=name.dat, | 22 count=name.dat, |
23 #end if | 23 #end if |
24 #if $group: | 24 #if $group: |
25 group=group.dat, | 25 group=group.dat, |
26 #end if | 26 #end if |
27 alpha=$alpha, | 27 alpha=$alpha, |
28 beta=$beta, | 28 beta=$beta, |
29 cutoff=$cutoff, | 29 cutoff=$cutoff, |
30 dereplicate=$dereplicate, | 30 dereplicate=$dereplicate, |
31 processors='\${GALAXY_SLOTS:-8}' | 31 processors='\${GALAXY_SLOTS:-8}' |
32 )' | 32 )' |
33 | sed 's/ //g' ## mothur trips over whitespace | 33 | sed 's/ //g' ## mothur trips over whitespace |
34 | mothur | 34 | mothur |
35 | tee mothur.out.log | 35 | tee mothur.out.log |
36 ]]></command> | 36 ]]></command> |
37 <inputs> | 37 <inputs> |
38 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/> | 38 <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/> |
39 <param name="name" type="data" format="mothur.names,mothur.count_table" label="name - Names or count_table"/> | 39 <param argument="name" type="data" format="mothur.names,mothur.count_table" label="name - Names or count_table"/> |
40 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> | 40 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> |
41 <param name="alpha" type="float" value="-5.54" label="alpha" help="The default is -5.54"/> | 41 <param argument="alpha" type="float" value="-5.54" label="alpha" help="The default is -5.54"/> |
42 <param name="beta" type="float" value="0.33" label="beta" help="The default is 0.33"/> | 42 <param argument="beta" type="float" value="0.33" label="beta" help="The default is 0.33"/> |
43 <param name="cutoff" type="float" value="0.50" label="cutoff" help="The default is 0.50"/> | 43 <param argument="cutoff" type="float" value="0.50" label="cutoff" help="The default is 0.50"/> |
44 <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric. default=false"/> | 44 <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups" |
45 help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric. default=false"/> | |
46 <expand macro="param-savelog"/> | |
45 </inputs> | 47 </inputs> |
46 <outputs> | 48 <outputs> |
47 <expand macro="logfile-output"/> | 49 <expand macro="logfile-output"/> |
48 <data name="out_chimeras" format="tabular" from_work_dir="fasta.perseus.chimeras" label="${tool.name} on ${on_string}: perseus.chimeras"/> | 50 <data name="out_chimeras" format="tabular" from_work_dir="fasta.perseus.chimeras" label="${tool.name} on ${on_string}: perseus.chimeras"/> |
49 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.perseus.accnos" label="${tool.name} on ${on_string}: perseus.accnos"/> | 51 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.perseus.accnos" label="${tool.name} on ${on_string}: perseus.accnos"/> |
51 <tests> | 53 <tests> |
52 <test> | 54 <test> |
53 <param name="fasta" value="amazon.fasta" ftype="fasta"/> | 55 <param name="fasta" value="amazon.fasta" ftype="fasta"/> |
54 <param name="name" value="amazon1.names" ftype="mothur.names"/> | 56 <param name="name" value="amazon1.names" ftype="mothur.names"/> |
55 <output name="out_chimeras" md5="bcd513127321a32035764a2087c23528" ftype="tabular"/> | 57 <output name="out_chimeras" md5="bcd513127321a32035764a2087c23528" ftype="tabular"/> |
58 <param name="savelog" value="true"/> | |
56 <expand macro="logfile-test"/> | 59 <expand macro="logfile-test"/> |
57 </test> | 60 </test> |
58 <!-- TODO: find/create test dataset with chimera present --> | 61 <!-- TODO: find/create test dataset with chimera present --> |
59 </tests> | 62 </tests> |
60 <help> | 63 <help><![CDATA[ |
61 <![CDATA[ | |
62 | 64 |
63 @MOTHUR_OVERVIEW@ | 65 @MOTHUR_OVERVIEW@ |
64 | 66 |
65 **Command Documentation** | 67 **Command Documentation** |
66 | 68 |
67 The chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences. | 69 The chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences. |
68 | 70 |
69 .. _chimera.perseus: https://www.mothur.org/wiki/Chimera.perseus | 71 .. _chimera.perseus: https://www.mothur.org/wiki/Chimera.perseus |
70 | 72 |
71 ]]> | 73 ]]></help> |
72 </help> | |
73 <expand macro="citations"/> | 74 <expand macro="citations"/> |
74 </tool> | 75 </tool> |