Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/chop.seqs.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
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1 <tool id="mothur_chop_seqs" name="Chop.seqs" version="1.20.0"> |
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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 --processors=8 |
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14 #if $name.__str__ != "None": |
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15 --name=$name |
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16 #end if |
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17 #if $group.__str__ != "None": |
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18 --group=$group |
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19 #end if |
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20 #if $count.__str__ != "None": |
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21 --count=$count |
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22 #end if |
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23 </command> |
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24 <inputs> |
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25 <param name="fasta" type="data" format="fasta,align" label="fasta - Sequences to be chopped"/> |
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26 <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/> |
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27 <param name="keep" type="select" label="keep - Part of the sequence to keep"> |
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28 <option value="front">front</option> |
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29 <option value="back">back</option> |
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30 </param> |
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31 <param name="countgaps" type="boolean" truevalue="--countgaps=true" falsevalue="" checked="false" label="countgaps - Count gaps as bases"/> |
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32 <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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33 <param name="name" type="data" format="name" label="name file" optional="true"/> |
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34 <param name="group" type="data" format="group" label="group file" optional="true"/> |
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35 <param name="count" type="data" format="count_table" label="count file" optional = "true"/> |
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36 </inputs> |
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37 <outputs> |
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38 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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39 <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" /> |
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40 </outputs> |
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41 <requirements> |
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42 <requirement type="package" version="1.33">mothur</requirement> |
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43 </requirements> |
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44 <tests> |
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45 </tests> |
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46 <help> |
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47 **Mothur Overview** |
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48 |
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49 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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50 in the Department of Microbiology and Immunology at The University of Michigan, |
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51 provides bioinformatics for the microbial ecology community. |
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52 |
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53 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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54 |
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55 **Command Documenation** |
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56 |
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57 The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences. |
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58 |
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59 .. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs |
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60 |
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61 v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0 |
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62 |
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63 </help> |
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64 </tool> |