Mercurial > repos > iuc > mothur_merge_taxsummary

annotate merge.taxsummary.xml @ 6:3a2ee62cb710 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author iuc
date Mon, 02 Dec 2019 06:47:37 -0500
parents 297f3f6ad488
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_merge_taxsummary" name="Merge.taxsummary" version="@WRAPPER_VERSION@.0">
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Merge tax.summary files</description>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
297f3f6ad488 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 #for $i in $input:
297f3f6ad488 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$i' input${input.index($i)}.dat &&
297f3f6ad488 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 #end for
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16
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17 echo 'merge.taxsummary(
297f3f6ad488 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 input=#for $i in $input#input${input.index($i)}.dat-#end for#,
297f3f6ad488 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 output=$output
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20 )'
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21 | sed 's/ //g' ## mothur trips over whitespace
297f3f6ad488 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 | sed 's/-,/,/g'
297f3f6ad488 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 | mothur
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24 | tee mothur.out.log
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8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 ]]></command>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 <inputs>
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27 <param name="input" type="data" format="mothur.tax.summary" multiple="true" label="input - tax.summary files"/>
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28 <expand macro="param-savelog"/>
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8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 </inputs>
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30 <outputs>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 <expand macro="logfile-output"/>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 <data name="output" format="mothur.tax.summary" label="${tool.name} on ${on_string}: merged sff"/>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 </outputs>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 <tests>
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35 <test>
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36 <param name="input" value="amazon.wang.knn.tax.summary,amazon.silva.wang.tax.summary"/>
2
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37 <output name="output" md5="7175d0709a1e4622d0710e79dd52801b" ftype="mothur.tax.summary"/>
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38 <param name="savelog" value="true"/>
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39 <expand macro="logfile-test"/>
8eebcd1d81b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 </test>
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41 </tests>
2
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42 <help><![CDATA[
0
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44 @MOTHUR_OVERVIEW@
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45
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46 .. _Mothur: https://www.mothur.org/wiki/Main_Page
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47
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48 **Command Documentation**
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49
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50 The merge.taxsummary command takes a list of tax.summary files separated by dashes and merges them into one file.
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51
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52 .. _merge.taxsummary: https://www.mothur.org/wiki/Merge.taxsummary
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53
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54 ]]></help>
0
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55 <expand macro="citations"/>
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56 </tool>