Mercurial > repos > workflow4metabolomics > w4mconcatenate
annotate concat.xml @ 0:c577f13705f2 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
| author | workflow4metabolomics |
|---|---|
| date | Wed, 10 Jul 2024 15:20:11 +0000 |
| parents | |
| children |
| rev | line source |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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1 <tool id="W4Mconcatenate" name="W4M concatenate" version="1.0.0+galaxy0"> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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2 <description>to merge two metadata tables</description> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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3 <requirements> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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4 <requirement type="package" version="4.3.3">r-base</requirement> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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changeset
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5 <requirement type="package" version="1.1.4">r-dplyr</requirement> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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6 <requirement type="package" version="1.0.0">r-w4mrutils</requirement> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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7 </requirements> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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8 <command detect_errors="exit_code"> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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9 <![CDATA[ |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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10 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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11 Rscript '$__tool_directory__/concatenation_wrapper.R' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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12 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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13 dataMatrix_1 '$dataMatrix_1' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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14 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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15 dataMatrix_2 '$dataMatrix_2' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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16 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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17 metadata_1 '$metadata_1' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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18 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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19 metadata_2 '$metadata_2' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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20 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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21 type '$type' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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22 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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23 tab1 '$tab1' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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24 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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25 tab2 '$tab2' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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26 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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27 concatenation '$concatenation' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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28 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
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29 choice_keep '$choice.choice_keep' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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30 #if str($choice.choice_keep) == 'yes': |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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31 keep 0 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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32 #end if |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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33 #if str($choice.choice_keep) == 'no': |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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34 keep "$choice.keep" |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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35 #end if |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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36 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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37 dataMatrix_1_out '$dataMatrix_1_out' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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38 dataMatrix_2_out '$dataMatrix_2_out' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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changeset
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39 metadata_out '$metadata_out' |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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40 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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41 ]]></command> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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42 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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43 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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44 <inputs> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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45 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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46 <param name="dataMatrix_1" type="data" label="Data matrix file 1" format="tabular"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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47 <param name="dataMatrix_2" type="data" label="Data matrix file 2" format="tabular"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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48 <param name="metadata_1" type="data" label="Metadata file 1" format="tabular"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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49 <param name="metadata_2" type="data" label="Metadata file 2" format="tabular"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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50 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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51 <param name="type" type="select" display="radio" label="Type of metadata"> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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52 <option value="sample">Sample metadata</option> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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53 <option value="variable">Variable metadata</option> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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54 </param> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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55 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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56 <param name="concatenation" type="select" display="radio" label="Type of concatenation"> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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57 <option value="unique">Unique</option> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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58 <option value="intersection">Intersection</option> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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59 <option value="union">Union</option> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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60 </param> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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61 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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62 <conditional name="choice"> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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63 <param name="choice_keep" type="select" display="radio" label="Keep all or just one"> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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64 <option value="yes">Keep all</option> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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65 <option value="no">Keep one</option> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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66 </param> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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67 <when value="no"> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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68 <param name="keep" type="select" display="radio" label="Which Metadata to keep"> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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69 <option value="1">Metadata 1</option> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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70 <option value="2">Metadata 2</option> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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71 </param> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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72 </when> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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73 <when value="yes"> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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74 </when> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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75 </conditional> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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76 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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77 <param name="tab1" type="text" label="Suffix for Metadata 1" value="Tab1"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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78 <param name="tab2" type="text" label="Suffix for Metadata 2" value="Tab2"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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79 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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80 </inputs> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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81 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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|
82 |
|
c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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|
83 |
|
c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
changeset
|
84 <outputs> |
|
c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
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|
85 |
|
c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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diff
changeset
|
86 <data name="dataMatrix_1_out" label="Concat_${dataMatrix_1.name}" format="tabular"></data> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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diff
changeset
|
87 <data name="dataMatrix_2_out" label="Concat_${dataMatrix_2.name}" format="tabular"></data> |
|
c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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diff
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88 <data name="metadata_out" label="Concat_${metadata_1.name}" format="tabular"></data> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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|
89 |
|
c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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diff
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|
90 </outputs> |
|
c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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|
91 |
|
c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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92 <tests> |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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|
93 <test> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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diff
changeset
|
94 <param name="dataMatrix_1" value="Input_Unique_Test_1-2-3-4-5_DM1.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
parents:
diff
changeset
|
95 <param name="dataMatrix_2" value="Input_Unique_Test_1-2-3_DM2.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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|
96 <param name="metadata_1" value="Input_Unique_Test_1_SM1.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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97 <param name="metadata_2" value="Input_Unique_Test_1_SM2.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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98 <param name="concatenation" value="unique"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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99 <param name="choice_keep" value="yes"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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100 <param name="tab1" value="tab1"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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101 <param name="tab2" value="tab2"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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102 |
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103 <output name="dataMatrix_1_out" file="Output_Attendu_Unique_Test_1-2-3_DM1.txt"/> |
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c577f13705f2
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104 <output name="dataMatrix_2_out" file="Output_Attendu_Unique_Test_1-2-3_DM2.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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105 <output name="metadata_out" file="Output_Attendu_Unique_Test_1_Metadata.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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106 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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107 |
|
c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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108 </test> |
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109 |
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c577f13705f2
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110 <test expect_failure="true"> |
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111 <param name="dataMatrix_1" value="Input_Unique_Test_1-2-3-4-5_DM1.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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112 <param name="dataMatrix_2" value="Input_Unique_Test_4_DM2.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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113 <param name="metadata_1" value="Input_Unique_Test_4_SM1.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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114 <param name="metadata_2" value="Input_Unique_Test_4_SM2.txt"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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115 <param name="concatenation" value="unique"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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116 <param name="choice_keep" value="yes"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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117 <param name="tab1" value="tab1"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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118 <param name="tab2" value="tab2"/> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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119 |
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120 </test> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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121 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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122 </tests> |
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123 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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124 <help><![CDATA[ |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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125 |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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126 .. class:: infomark |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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127 |
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128 **Credits** |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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129 | **Original tool code:** Hanane Nourine |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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130 | **Original tool wrapping:** Hanane Nourine |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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131 | **Tool maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB) |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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132 | **Wrapper maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB) |
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133 |
|
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134 .. class:: infomark |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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135 |
|
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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136 **Contact:** Melanie Petera (PFEM - INRAE - MetaboHUB) |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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|
137 |
|
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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|
138 --------------------------------------------------- |
|
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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139 |
|
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|
140 ****************** |
|
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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141 Concatenation |
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142 ****************** |
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143 |
|
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|
144 =========== |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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145 DESCRIPTION |
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146 =========== |
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147 |
|
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148 Concatenate two Metadata tables |
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149 |
|
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|
150 |
|
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|
151 --------------------------------------------------- |
|
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152 |
|
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|
153 ========================== |
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154 ALIGNMENT WITH OTHER TOOLS |
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|
155 ========================== |
|
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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156 |
|
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157 This tool is designed to work with the W4M 3-tables format. Inputs are supposed to follow this standard. |
|
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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158 Outputs follows the standard and thus can be used in further W4M-supported workflows. |
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|
159 |
|
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|
160 ----------- |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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161 Input files |
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|
162 ----------- |
|
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163 |
|
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164 +----------------------------------+------------+ |
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165 | Parameter : num + label | Format | |
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166 +==================================+============+ |
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167 | 1 : First Data matrix file | tabular | |
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168 +----------------------------------+------------+ |
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169 | 2 : First metadata file | tabular | |
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170 +----------------------------------+------------+ |
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171 | 3 : Second Data matrix file | tabular | |
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172 +----------------------------------+------------+ |
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173 | 4 : Second metadata file | tabular | |
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174 +----------------------------------+------------+ |
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175 |
|
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176 ------------ |
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177 Output files |
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178 ------------ |
|
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179 |
|
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180 +----------------------------------+------------+ |
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181 | Parameter : num + label | Format | |
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182 +==================================+============+ |
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183 | 1 : Metadata concatenate file | tabular | |
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184 +----------------------------------+------------+ |
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185 | 2 : First Data matrix file | tabular | |
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186 +----------------------------------+------------+ |
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187 | 3 : Second Data matrix file | tabular | |
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188 +----------------------------------+------------+ |
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189 |
|
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190 --------------------------------------------------- |
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191 |
|
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192 |
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193 =============== |
|
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194 TOOL PARAMETERS |
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195 =============== |
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196 |
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197 |
|
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198 Data matrix |
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199 | contains the intensity values of the analytical variables. |
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200 | First line is the sample identifiers and first column the variable identifiers. |
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201 | |
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202 |
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203 |
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204 Metadata file |
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205 | contains metadata about samples OR variables (only one type possible at a time). |
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206 | Each metadata file must match its corresponding data matrix file regarding identifiers. |
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207 | |
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208 |
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209 Type of metadata |
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210 | Specify which type of metadata table is given as metadata file |
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211 | |
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212 |
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213 |
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214 Type of concatenation |
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215 | Selects the type of concatenation |
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216 | Unique: identifiers are the same in both datasets (i.e. metadata file 1 and metadata file 2 are expected to match perfectly regarding identifiers) |
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217 | Intersection: keep only identifiers in common |
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218 | Union: keep all identifiers in both datasets |
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219 | |
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220 |
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221 Choice_keep |
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222 | Determine what to do in case a column name is found in the two metadata files |
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223 | - Keep all: both columns and change their names by adding a prefix |
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224 | - Keep one: the column belonging to metadata 1 or metadata 2 |
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225 | |
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226 |
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227 Prefixes for redundant columns |
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228 | By default, the prefixes are Tab1 and Tab2 |
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229 | |
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230 |
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231 ================== |
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232 OUTPUT DESCRIPTION |
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233 ================== |
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234 |
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235 **Unique**: the tables must have the same identifiers, otherwise a warning will be generated. |
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236 The output returned is a unique merged metadata file without modifying the DataMatrices. |
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237 |
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238 **Intersection**: there must be identifiers in common between the two metadata tables, otherwise an error will be displayed. |
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239 Moreover, if the number of identifiers in common is less than 5, a warning will be generated. |
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240 The DataMatrix outputs will only keep common identifiers. |
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241 |
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242 **Union**: the identifiers don't necessarily have to be the same between the metadata tables. If no identifiers are common, a warning will be generated. |
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243 The modified DataMatrix will then include all the individuals, adding NA values for those that are missing. |
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244 If common pairs of sample and variable exist between the dataset 1 and dataset 2 with no difference in the intensity values, |
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245 the intersections will be added instead of NA. |
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246 |
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247 |
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248 |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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249 ]]></help> |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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250 <citations> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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251 <citation type="doi">10.1093/bioinformatics/btu813</citation> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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252 </citations> |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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253 |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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254 <creator> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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255 <organization name="PFEM" url="https://eng-pfem.isc.inrae.fr/"></organization> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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256 <organization name="Workflow4metabolomics" url="https://workflow4metabolomics.org/"></organization> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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257 |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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258 <person givenName="Hanane" familyName="Nourine" jobTitle="Intern"></person> |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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259 <person givenName="Mélanie" familyName="Petera"></person> |
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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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260 </creator> |
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c577f13705f2
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
workflow4metabolomics
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261 </tool> |