Mercurial > repos > iuc > mothur_shhh_seqs
comparison shhh.seqs.xml @ 2:c54bf33450d7 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 22:17:05 -0400 |
parents | fddd81ee5cd4 |
children | 6ee54b761c3c |
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1:c7e60f5aadcb | 2:c54bf33450d7 |
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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 "$fasta" fasta.dat && | 13 ln -s '$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 'shhh.seqs( | 17 echo 'shhh.seqs( |
18 fasta=fasta.dat, | 18 fasta=fasta.dat, |
19 name=name.dat, | 19 name=name.dat, |
20 #if $group: | 20 #if $group: |
21 group=group.dat, | 21 group=group.dat, |
22 #end if | 22 #end if |
23 sigma=$sigma, | 23 sigma=$sigma, |
24 processors='\${GALAXY_SLOTS:-8}' | 24 processors='\${GALAXY_SLOTS:-8}' |
25 )' | 25 )' |
26 | sed 's/ //g' ## mothur trips over whitespace | 26 | sed 's/ //g' ## mothur trips over whitespace |
27 | mothur | 27 | mothur |
28 | tee mothur.out.log | 28 | tee mothur.out.log |
29 ]]></command> | 29 ]]></command> |
30 <inputs> | 30 <inputs> |
31 <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/> | 31 <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/> |
32 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> | 32 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> |
33 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> | 33 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> |
34 <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/> | 34 <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/> |
35 <expand macro="param-savelog"/> | |
35 </inputs> | 36 </inputs> |
36 <outputs> | 37 <outputs> |
37 <expand macro="logfile-output"/> | 38 <expand macro="logfile-output"/> |
38 <data name="shhh_fasta" format_source="fasta" from_work_dir="fasta*.shhh_seqs.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/> | 39 <data name="shhh_fasta" format_source="fasta" from_work_dir="fasta*.shhh_seqs.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/> |
39 <data name="shhh_names" format="mothur.names" from_work_dir="fasta*.shhh_seqs.names" label="${tool.name} on ${on_string}: shhh.names"/> | 40 <data name="shhh_names" format="mothur.names" from_work_dir="fasta*.shhh_seqs.names" label="${tool.name} on ${on_string}: shhh.names"/> |
44 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/> | 45 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/> |
45 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names"/> | 46 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names"/> |
46 <output name="shhh_fasta" md5="0169152fa33b588cabf3c3b932cc6018" ftype="mothur.align"/> | 47 <output name="shhh_fasta" md5="0169152fa33b588cabf3c3b932cc6018" ftype="mothur.align"/> |
47 <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/> | 48 <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/> |
48 <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/> | 49 <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/> |
50 <param name="savelog" value="true"/> | |
49 <expand macro="logfile-test"/> | 51 <expand macro="logfile-test"/> |
50 </test> | 52 </test> |
51 </tests> | 53 </tests> |
52 <help> | 54 <help><![CDATA[ |
53 <![CDATA[ | |
54 | 55 |
55 @MOTHUR_OVERVIEW@ | 56 @MOTHUR_OVERVIEW@ |
56 | 57 |
57 **Command Documentation** | 58 **Command Documentation** |
58 | 59 |
59 The shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise. Schloss prefers pre.cluster for this operation. | 60 The shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise. Schloss prefers pre.cluster for this operation. |
60 | 61 |
61 .. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs | 62 .. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs |
62 | 63 |
63 ]]> | 64 ]]></help> |
64 </help> | |
65 <expand macro="citations"/> | 65 <expand macro="citations"/> |
66 </tool> | 66 </tool> |