Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/summary.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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1 <tool id="mothur_summary_seqs" name="Summary.seqs" version="1.19.0"> |
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2 <description>Summarize the quality of sequences</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='summary.seqs' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$out_summary |
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7 --outputdir='$logfile.extra_files_path' |
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8 --fasta=$fasta |
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9 #if $name.__str__ != "None" and len($name.__str__) > 0: |
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10 --name=$name |
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11 #end if |
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12 --processors=8 |
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13 </command> |
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14 <inputs> |
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15 <param name="fasta" type="data" format="fasta,align" label="fasta - Dataset"/> |
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16 <param name="name" type="data" format="names" label="name - Names" optional="true"/> |
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17 </inputs> |
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18 <outputs> |
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19 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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20 <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" /> |
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21 </outputs> |
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22 <requirements> |
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23 <requirement type="package" version="1.27">mothur</requirement> |
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24 </requirements> |
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25 <tests> |
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26 </tests> |
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27 <help> |
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28 **Mothur Overview** |
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29 |
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30 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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31 in the Department of Microbiology and Immunology at The University of Michigan, |
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32 provides bioinformatics for the microbial ecology community. |
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33 |
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34 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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35 |
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36 **Command Documenation** |
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37 |
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38 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. |
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39 |
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40 |
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41 .. _summary.seqs: http://www.mothur.org/wiki/Summary.seqs |
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42 |
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43 </help> |
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44 </tool> |