Mercurial > repos > iuc > mothur_merge_count

annotate merge.count.xml @ 8:d7e3ae575b95 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 23:08:00 +0000
parents af4ee04768b0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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1 <tool profile="16.07" id="mothur_merge_count" name="Merge.count" version="@WRAPPER_VERSION@.0">
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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2 <description>Merge count tables</description>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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3 <macros>
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4 <import>macros.xml</import>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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5 </macros>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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6 <expand macro="requirements"/>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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7 <expand macro="stdio"/>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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8 <expand macro="version_command"/>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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9 <command><![CDATA[
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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10 @SHELL_OPTIONS@
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11
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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12 ## create symlinks to input datasets
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 #for $i in $input:
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$i' input${input.index($i)}.dat &&
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 #end for
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16
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17 echo 'merge.count(
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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18 count=#for $i in $input#input${input.index($i)}.dat-#end for#,
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 output=$output
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 )'
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 | sed 's/ //g' ## mothur trips over whitespace
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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22 | sed 's/-,/,/g'
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 | mothur
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 | tee mothur.out.log
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 ]]></command>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 <inputs>
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27 <param name="input" type="data" format="mothur.count_table" multiple="true" label="input - count tables to merge"/>
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28 <expand macro="param-savelog"/>
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41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 </inputs>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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30 <outputs>
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31 <expand macro="logfile-output"/>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 <data name="output" format="mothur.count_table" label="${tool.name} on ${on_string}: merged count table"/>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="stool_small.count_table,amazon.count_table"/>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 <output name="output" ftype="mothur.count_table">
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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38 <assert_contents>
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39 <expand macro="test-count-format"/>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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40 <has_text text="U68630"/>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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41 <has_text text="F11Fcsw_12747"/>
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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42 </assert_contents>
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43 </output>
1
af4ee04768b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
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44 <param name="savelog" value="true"/>
0
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45 <expand macro="logfile-test"/>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49
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50 @MOTHUR_OVERVIEW@
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51
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52 .. _Mothur: https://www.mothur.org/wiki/Main_Page
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53
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54 **Command Documentation**
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55
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56 The merge.count_ command merges count files into a single count table.
41c7989dd5e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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57
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58 .. _merge.count: https://www.mothur.org/wiki/Merge.count
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59
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60 ]]></help>
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61 <expand macro="citations"/>
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62 </tool>