annotate merge.sfffiles.xml @ 3:28eb204d497d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author iuc
date Fri, 06 Apr 2018 04:14:32 -0400
parents e0d980518148
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e7f1da3e0339 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_sfffiles" name="Merge.sfffiles" version="@WRAPPER_VERSION@.0">
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2 <description>Merge SFF files</description>
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3 <macros>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
e7f1da3e0339 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"/>
e7f1da3e0339 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
2
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12 ## create symlinks to input datasets
e0d980518148 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 #for $i in $input:
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14 ln -s '$i' input${input.index($i)}.dat &&
e0d980518148 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.sfffiles(
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18 sff=#for $i in $input#input${input.index($i)}.dat-#end for#,
e0d980518148 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 output=$output
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20 )'
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21 | sed 's/ //g' ## mothur trips over whitespace
e0d980518148 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 | sed 's/-,/,/g'
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23 | mothur
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24 | tee mothur.out.log
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25 ]]></command>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 <inputs>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/>
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28 <expand macro="param-savelog"/>
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29 </inputs>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 <outputs>
e7f1da3e0339 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"/>
e7f1da3e0339 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="sff" label="${tool.name} on ${on_string}: merged sff"/>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 </outputs>
e7f1da3e0339 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="Fasting_Example1.sff,Fasting_Example2.sff"/>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <output name="output" ftype="sff">
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <assert_contents>
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39 <has_text text="FLP3FBN01ELBSX"/>
e7f1da3e0339 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 </assert_contents>
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41 </output>
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42 <param name="savelog" value="true"/>
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43 <expand macro="logfile-test"/>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47
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48 @MOTHUR_OVERVIEW@
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49
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50 .. _Mothur: https://www.mothur.org/wiki/Main_Page
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51
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52 **Command Documentation**
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53
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54 The merge.sfffiles_ command merge inputs into a single output.
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55
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56 .. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles
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57
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58 ]]></help>
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59 <expand macro="citations"/>
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60 </tool>