Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/degap.seqs.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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7 | 1 <tool id="mothur_degap_seqs" name="Degap.seqs" version="1.20.0"> |
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2 <description>Remove gap characters from sequences</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='degap.seqs' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+.ng\.\w+$:'$out_fasta |
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7 --outputdir='$logfile.extra_files_path' |
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8 --fasta=$fasta |
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9 </command> |
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10 <inputs> |
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11 <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/> |
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12 </inputs> |
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13 <outputs> |
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14 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
4 | 15 <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> |
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16 </outputs> |
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17 <requirements> |
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18 <requirement type="package" version="1.27">mothur</requirement> |
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19 </requirements> |
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20 <tests> |
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21 </tests> |
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22 <help> |
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23 **Mothur Overview** |
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24 |
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25 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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26 in the Department of Microbiology and Immunology at The University of Michigan, |
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27 provides bioinformatics for the microbial ecology community. |
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28 |
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29 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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30 |
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31 **Command Documenation** |
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32 |
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33 The degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed. |
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34 |
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35 .. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs |
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36 |
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37 |
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38 </help> |
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39 </tool> |