Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/chop.seqs.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
parents | 3202a38e44d9 |
children | e990ac8a0f58 |
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Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_chop_seqs" name="Chop.seqs" version="1.16.0"> |
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2 <description>Trim sequences to a specified length</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='chop.seqs' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+.chop\.fasta$:'$out_fasta |
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7 --outputdir='$logfile.extra_files_path' |
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8 --fasta=$fasta |
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9 --numbases=$numbases |
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10 --keep=$keep |
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11 $countgaps |
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12 $short |
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13 </command> |
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14 <inputs> |
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15 <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/> |
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16 <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/> |
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17 <param name="keep" type="select" label="keep - Part of the sequence to keep"> |
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18 <option value="front">front</option> |
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19 <option value="back">back</option> |
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20 </param> |
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21 <param name="countgaps" type="boolean" truevalue="--countgaps=true" falsevalue="" checked="false" label="countgaps - Count gaps as bases"/> |
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22 <param name="short" type="boolean" truevalue="--short=true" falsevalue="" checked="false" label="short - keep sequences that are too short to chop"/> |
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23 </inputs> |
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24 <outputs> |
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25 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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26 <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" /> |
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27 </outputs> |
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28 <requirements> |
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29 <requirement type="binary">mothur</requirement> |
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30 </requirements> |
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31 <tests> |
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32 </tests> |
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33 <help> |
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34 **Mothur Overview** |
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35 |
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36 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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37 in the Department of Microbiology and Immunology at The University of Michigan, |
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38 provides bioinformatics for the microbial ecology community. |
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39 |
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40 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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41 |
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42 **Command Documenation** |
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43 |
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44 The chop.seqs_ command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. It works on both aligned and unaligned sequences. |
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45 |
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46 .. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs |
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47 |
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48 |
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49 </help> |
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50 </tool> |