Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/merge.files.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 49058b1f8d3f |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_merge_files" name="Merge.files" version="1.19.0"> |
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2 <description>Merge data</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='merge.files' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'mergefile:'$output |
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7 --outputdir='$logfile.extra_files_path' |
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8 --input=${merge.input}#for i in $merge.inputs#,${i.input}#end for# |
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9 --output='mergefile' |
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10 </command> |
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11 <inputs> |
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12 <conditional name="merge"> |
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13 <param name="type" type="select" format="fasta,qual,groups,names,accnos" label="Merge"> |
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14 <option value="fasta">fasta</option> |
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15 <option value="qual">qual</option> |
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16 <option value="groups">groups</option> |
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17 <option value="names">names</option> |
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18 <option value="accnos">accnos</option> |
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19 </param> |
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20 <when value="fasta"> |
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21 <param name="input" type="data" format="fasta" label="input - fasta"/> |
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22 <repeat name="inputs" title="And fasta"> |
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23 <param name="input" type="data" format="fasta" label="input - fasta"/> |
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24 </repeat> |
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25 </when> <!-- fasta --> |
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26 <when value="qual"> |
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27 <param name="input" type="data" format="qual" label="input - qual"/> |
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28 <repeat name="inputs" title="And qual"> |
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29 <param name="input" type="data" format="qual" label="input - qual"/> |
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30 </repeat> |
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31 </when> <!-- qual --> |
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32 <when value="groups"> |
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33 <param name="input" type="data" format="groups" label="input - groups"/> |
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34 <repeat name="inputs" title="And group"> |
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35 <param name="input" type="data" format="groups" label="input - groups"/> |
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36 </repeat> |
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37 </when> <!-- groups --> |
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38 <when value="names"> |
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39 <param name="input" type="data" format="names" label="input - names"/> |
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40 <repeat name="inputs" title="And name"> |
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41 <param name="input" type="data" format="names" label="input - names"/> |
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42 </repeat> |
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43 </when> <!-- names --> |
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44 <when value="accnos"> |
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45 <param name="input" type="data" format="accnos" label="input - accnos"/> |
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46 <repeat name="inputs" title="And accno"> |
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47 <param name="input" type="data" format="accnos" label="input - accnos"/> |
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48 </repeat> |
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49 </when> <!-- fasta --> |
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50 </conditional> <!-- merge --> |
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51 </inputs> |
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52 <outputs> |
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53 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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54 <data format="input" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/> |
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55 </outputs> |
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56 <requirements> |
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57 <requirement type="binary">mothur</requirement> |
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58 </requirements> |
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59 <tests> |
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60 </tests> |
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61 <help> |
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62 **Mothur Overview** |
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63 |
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64 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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65 in the Department of Microbiology and Immunology at The University of Michigan, |
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66 provides bioinformatics for the microbial ecology community. |
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67 |
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68 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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69 |
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70 **Command Documenation** |
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71 |
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72 The merge.files_ command merge inputs into a single output. |
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73 |
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74 .. _merge.files: http://www.mothur.org/wiki/Merge.files |
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75 |
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76 |
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77 </help> |
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78 </tool> |