Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/degap.seqs.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
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34:1be61ceb20d7 | 35:95d75b35e4d2 |
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1 <tool id="mothur_degap_seqs" name="Degap.seqs" version="1.20.0"> | 1 <tool id="mothur_degap_seqs" name="Degap.seqs" version="1.21.0"> |
2 <description>Remove gap characters from sequences</description> | 2 <description>Remove gap characters from sequences</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='degap.seqs' | 5 --cmd='degap.seqs' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+.ng\.\w+$:'$out_fasta | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+.ng\.\w+$:'$out_fasta |
13 <outputs> | 13 <outputs> |
14 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 14 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
15 <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> | 15 <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> |
16 </outputs> | 16 </outputs> |
17 <requirements> | 17 <requirements> |
18 <requirement type="package" version="1.27">mothur</requirement> | 18 <requirement type="package" version="1.33">mothur</requirement> |
19 </requirements> | 19 </requirements> |
20 <tests> | 20 <tests> |
21 </tests> | 21 </tests> |
22 <help> | 22 <help> |
23 **Mothur Overview** | 23 **Mothur Overview** |
32 | 32 |
33 The degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed. | 33 The degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed. |
34 | 34 |
35 .. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs | 35 .. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs |
36 | 36 |
37 v1.21.0: Updated to Mothur 1.33 | |
38 | |
37 | 39 |
38 </help> | 40 </help> |
39 </tool> | 41 </tool> |