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author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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1 <tool profile="16.07" id="mothur_make_lefse" name="Make.lefse" version="@WRAPPER_VERSION@.0">
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2 <description>create a lefse formatted input file from mothur's output files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 echo 'make.lefse(
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10 #if $otu.is_of_type("mothur.relabund"):
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11 relabund=$otu,
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12 #else
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13 shared=$otu,
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14 #end if
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15 #if $design:
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16 design=$design,
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17 #end if
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18 #if $constaxonomy:
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19 constaxonomy=$constaxonomy,
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20 #end if
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21 #if $label:
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22 label=${ str($label).replace(",","-") },
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23 #end if
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24 scale=$scale
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25 )'
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26 | sed 's/ //g' ## mothur trips over whitespace
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27 | mothur &&
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28
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29 ## move output files to correct destination
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30 prefix="$otu" &&
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31 mv \${prefix%.dat}*.lefse "$lefse_out" &&
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32 mv mothur.*.logfile "$logfile"
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33 ]]></command>
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34 <inputs>
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35 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/>
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36 <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
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37 <expand macro="labeloptions"/>
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38 </param>
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39 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="constaxonomy - provide a constaxonomy file"/>
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40 <param name="design" type="data" format="tabular" optional="true" label="design - provide your design file"/>
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41 <param name="scale" type="select" multiple="false" label="scale - select what scale you would like to use to convert your shared file abundances to relative abundances" help="">
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42 <option value="totalgroup" selected="true">totalgroup</option>
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43 <option value="totalotu">totalotu</option>
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44 <option value="averagegroup">averagegroup</option>
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45 <option value="averageotu">averageotu</option>
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46 </param>
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47 </inputs>
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48 <outputs>
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49 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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50 <data name="lefse_out" format="tabular" label="${tool.name} on ${on_string}: lefse"/>
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51 </outputs>
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52 <tests>
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53 <test><!-- test with shared file and defaults -->
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54 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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55 <output name="lefse_out" md5="295633107cd983be73389e8b92164686" ftype="tabular"/>
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56 <expand macro="logfile-test"/>
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57 </test>
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58 <test><!-- test with relabund file -->
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59 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
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60 <param name="design" value="toymothur.design2" ftype="tabular"/>
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61 <param name="label" value="0.18"/>
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62 <output name="lefse_out" md5="c1e88702c6db198080c09f3b9c404c63" ftype="tabular"/>
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63 <expand macro="logfile-test"/>
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64 </test>
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65 </tests>
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66 <help>
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67 <![CDATA[
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68
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69 @MOTHUR_OVERVIEW@
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70
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71 **Command Documenation**
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72
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73 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files.
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74
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75 .. _make.lefse: http://www.mothur.org/wiki/Make.lefse
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76
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77 ]]>
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78 </help>
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79 <citations>
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80 <citation type="doi">10.1128/AEM.01541-09</citation>
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81 </citations>
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82 </tool>