Mercurial > repos > iuc > humann2_regroup_table
annotate humann2_regroup_table.xml @ 0:a1747df2bc21 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
author | iuc |
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date | Mon, 13 Mar 2017 12:38:02 -0400 |
parents | |
children | 1d141730ec69 |
rev | line source |
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0
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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1 <tool id="humann2_regroup_table" name="Regroup" version="@WRAPPER_VERSION@.0"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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2 <description> a HUMAnN2 generated table by features</description> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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3 <macros> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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4 <import>humann2_macros.xml</import> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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5 </macros> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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6 <expand macro="requirements"/> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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7 <expand macro="version"/> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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9 humann2_regroup_table |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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10 --input '$input' |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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11 -o '$output_table' |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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12 --function '$function' |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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13 |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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14 #if $built_in.built_in_test == "true": |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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15 --groups '$built_in.gene_family_groups.groups' |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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16 #else: |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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17 --custom '$built_in.custom' |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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18 $built_in.reversed |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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19 #end if |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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20 |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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21 --ungrouped '$ungrouped' |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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22 --protected '$protected' |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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23 ]]></command> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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24 <inputs> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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25 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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26 <param argument="--function" type="select" label="How to combine grouped features?"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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27 <option value="sum" selected="true">Sum</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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28 <option value="mean">Mean</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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29 </param> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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30 <conditional name="built_in"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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31 <param name="built_in_test" type="select" label="Use built-in grouping options?" help=""> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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32 <option value="true" selected="true">Yes</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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33 <option value="false">No</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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34 </param> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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35 <when value="true"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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36 <conditional name="gene_family_groups"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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37 <param name="gene_family_type" type="select" label="Gene family type"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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38 <option value="uniref50">UniRef50 gene families</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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39 <option value="uniref90">UniRef90 gene families</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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40 </param> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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41 <when value="uniref50"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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42 <param name="groups" type="select" label="Grouping options" help="(--groups)"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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43 <option value="uniref50_go">UniRef50 gene families into GO</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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44 <option value="uniref50_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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45 <option value="uniref50_eggnog">UniRef50 gene families into eggNOG</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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46 <option value="uniref50_pfam">UniRef50 gene families into PFAM</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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47 <option value="uniref50_level4ec">UniRef50 gene families into level4ec</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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48 <option value="uniref50_infogo1000">UniRef50 gene families into InfoGO1000</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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49 <option value="uniref50_rxn">UniRef50 gene families into metacyc reactions</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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50 </param> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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51 </when> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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52 <when value="uniref90"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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53 <param name="groups" type="select" label="Grouping options" help="(--groups)"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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54 <option value="uniref90_go">UniRef90 gene families into GO</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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55 <option value="uniref90_ko">UniRef90 gene families into KEGG Orthogroups (KOs)</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
changeset
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56 <option value="uniref90_eggnog">UniRef90 gene families into eggNOG</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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57 <option value="uniref90_pfam">UniRef90 gene families into PFAM</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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58 <option value="uniref90_level4ec">UniRef90 gene families into level4ec</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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59 <option value="uniref90_infogo1000">UniRef90 gene families into InfoGO1000</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
diff
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60 <option value="uniref90_rxn">UniRef90 gene families into metacyc reactions</option> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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61 </param> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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62 </when> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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63 </conditional> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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64 </when> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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65 <when value="false"> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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66 <param argument="--custom" type="data" format="tsv" label="Custom groups file"/> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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67 <param argument="--reversed" type="boolean" checked="false" truevalue="--reversed" falsevalue="" label="Is the groups file reversed?" help="Mapping from features to groups"/> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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68 </when> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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69 </conditional> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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70 <param argument="--precision" type="integer" value="3" label="Decimal places to round to after applying function"/> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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71 <param argument="--ungrouped" type="boolean" checked="true" truevalue="Y" falsevalue="N" label="Include an 'UNGROUPED' group to capture features that did not belong to other groups?"/> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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72 <param argument="--protected" type="boolean" checked="true" truevalue="Y" falsevalue="N" label="Carry through protected features, such as 'UNMAPPED'?"/> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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73 </inputs> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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74 <outputs> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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75 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Regrouped table" /> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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76 </outputs> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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77 <tests> |
a1747df2bc21
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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78 <test> |
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79 <param name="input" value="demo_genefamilies.tsv"/> |
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80 <param name="function" value="sum"/> |
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81 <param name="built_in_test" value="true"/> |
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82 <param name="gene_family_type" value="uniref90"/> |
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83 <param name="groups" value="uniref90_infogo1000"/> |
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84 <param name="ungrouped" value="Y"/> |
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85 <param name="protected" value="Y"/> |
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86 <output name="output_table" file="regrouped_gene_families_to_infogo1000.tsv"/> |
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87 </test> |
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88 <test> |
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89 <param name="input" value="demo_genefamilies.tsv"/> |
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90 <param name="function" value="mean"/> |
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91 <param name="built_in_test" value="true"/> |
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92 <param name="gene_family_type" value="uniref90"/> |
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93 <param name="groups" value="uniref90_ko"/> |
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94 <param name="ungrouped" value="Y"/> |
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95 <param name="protected" value="Y"/> |
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96 <output name="output_table" file="regrouped_gene_families_to_ko.tsv"/> |
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97 </test> |
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98 <test> |
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99 <param name="input" value="demo_genefamilies.tsv"/> |
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100 <param name="function" value="sum"/> |
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101 <param name="built_in_test" value="true"/> |
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102 <param name="gene_family_type" value="uniref90"/> |
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103 <param name="groups" value="uniref90_rxn"/> |
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104 <param name="ungrouped" value="Y"/> |
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105 <param name="protected" value="Y"/> |
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106 <output name="output_table" file="regrouped_gene_families_to_rxn.tsv"/> |
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107 </test> |
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108 </tests> |
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109 <help><![CDATA[ |
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110 @HELP_HEADER@ |
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111 |
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112 Regroup HUMAnN2 table features is a tool for regrouping table features (abundances or coverage) given a table of feature values and a mapping of groups to component features. It produces a new table with group values in place of feature values. |
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113 ]]></help> |
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114 <expand macro="citations"/> |
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115 </tool> |