Mercurial > repos > sanbi-uwc > mothur_test

annotate tools/mothur/merge.files.xml @ 0:ee4fee239fe7 draft default tip

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planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool profile="16.07" id="mothur_merge_files" name="Merge.files" version="@WRAPPER_VERSION@.0">
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2 <description>Merge data</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 #set infiles=str($merge.inputs).replace(',','-').replace(' ','')
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10 echo 'merge.files(
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11 input=$infiles,
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12 output=$output
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13 )'
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14 | sed 's/ //g' ## mothur trips over whitespace
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15 | mothur &&
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16
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17 ## move output files to correct destination
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18 mv mothur.*.logfile "$logfile"
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19 ]]></command>
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20 <inputs>
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21 <conditional name="merge">
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22 <param name="type" type="select" format="fasta,qual,mothur.groups,mothur.names,mothur.accnos" label="Merge">
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23 <option value="fasta">fasta</option>
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24 <option value="qual">qual</option>
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25 <option value="groups">groups</option>
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26 <option value="names">names</option>
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27 <option value="accnos">accnos</option>
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28 </param>
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29 <when value="fasta">
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30 <param name="inputs" type="data" format="fasta" multiple="true" label="inputs - fasta"/>
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31 </when> <!-- fasta -->
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32 <when value="qual">
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33 <param name="inputs" type="data" format="qual" multiple="true" label="inputs - qual"/>
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34 </when> <!-- qual -->
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35 <when value="groups">
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36 <param name="inputs" type="data" format="mothur.groups" multiple="true" label="inputs - groups"/>
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37 </when> <!-- groups -->
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38 <when value="names">
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39 <param name="inputs" type="data" format="mothur.names" multiple="true" label="inputs - names"/>
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40 </when> <!-- names -->
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41 <when value="accnos">
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42 <param name="inputs" type="data" format="mothur.accnos" multiple="true" label="inputs - accnos"/>
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43 </when> <!-- fasta -->
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44 </conditional> <!-- merge -->
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45 </inputs>
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46 <outputs>
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47 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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48 <data format_source="inputs" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="type" value="fasta"/>
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53 <param name="inputs" value="sample1.fa,sample2.fa,sample3.fa" ftype="fasta"/>
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54 <output name="output" file="output.fa" ftype="fasta"/>
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55 <expand macro="logfile-test"/>
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56 </test>
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57 </tests>
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58 <help>
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59 @MOTHUR_OVERVIEW@
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60
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61 **Command Documenation**
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62
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63 The merge.files_ command merge inputs into a single output.
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64
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65 .. _merge.files: http://www.mothur.org/wiki/Merge.files
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66
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67
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68 </help>
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69 <expand macro="citations"/>
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70 </tool>