Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/align.check.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_align_check" name="Align.check" version="1.20.0"> |
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2 <description>Calculate the number of potentially misaligned bases</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='align.check' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align\.check$:'$out_file |
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7 --outputdir='$logfile.extra_files_path' |
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8 --fasta=$fasta |
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9 --map=$ss.map |
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10 #if $count.__str__ != "None" and len($count.__str__) >0: |
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11 --count=$count |
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12 #end if |
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13 #if $count.__str__ != "None" and len($count.__str__) >0: |
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14 --name=$name |
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15 #end if |
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16 |
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17 </command> |
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18 <inputs> |
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19 <param name="fasta" type="data" format="align" label="fasta - Aligned Sequences"/> |
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20 <conditional name="ss"> |
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21 <param name="source" label="Select Secondary Structure Map from" type="select"> |
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22 <option value="cached">Cached Secondary Structure Maps</option> |
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23 <option value="history">Your History</option> |
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24 </param> |
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25 <when value="cached"> |
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26 <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions"> |
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27 <options from_data_table="mothur_map"> |
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28 </options> |
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29 </param> |
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30 </when> |
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31 <when value="history"> |
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32 <param name="map" format="map" type="data" label="Secondary Structure Map" /> |
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33 </when> |
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34 </conditional> |
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35 <param name="count" type="data" format="count_table" label="count_table file" optional="true" help="You can also provide a name file associated with your fasta file"/> |
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36 <param name="name" type="data" format="names" label="names file" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/> |
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37 </inputs> |
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38 <outputs> |
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39 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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40 <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/> |
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41 </outputs> |
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42 <requirements> |
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43 <requirement type="package" version="1.33">mothur</requirement> |
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44 </requirements> |
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45 <tests> |
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46 </tests> |
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47 <help> |
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48 **Mothur Overview** |
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49 |
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50 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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51 in the Department of Microbiology and Immunology at The University of Michigan, |
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52 provides bioinformatics for the microbial ecology community. |
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53 |
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54 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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55 |
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56 **Command Documenation** |
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57 |
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58 The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment using a secondary_structure_map_. If you are familiar with the editor window in ARB, this is the same as counting the number of ~, #, -, and = signs. |
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59 |
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60 .. _secondary_structure_map: http://www.mothur.org/wiki/Secondary_structure_map |
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61 .. _align.check: http://www.mothur.org/wiki/Align.check |
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62 |
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63 </help> |
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64 </tool> |