annotate recetox_aplcms_compute_template.xml @ 0:38469e025939 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
author recetox
date Mon, 13 Feb 2023 10:27:35 +0000
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children 51e37adf988f
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38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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1 <tool id="recetox_aplcms_compute_template" name="recetox-aplcms - compute template" version="@TOOL_VERSION@+galaxy0">
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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2 <description>compute retention time correction template feature table</description>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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3 <macros>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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4 <import>macros.xml</import>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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5 <import>help.xml</import>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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6 </macros>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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7 <expand macro="creator"/>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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8 <expand macro="requirements"/>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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10 <command detect_errors="aggressive"><![CDATA[
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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11 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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12 ]]></command>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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13 <configfiles>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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14 <configfile name="run_script"><![CDATA[
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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15 #set filenames = str("', '").join([str($f) for $f in $files])
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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16 feature_tables <- load_parquet_collection(c('$filenames'))
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38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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18 template_features <- compute_template(feature_tables)
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20 save_data_as_parquet_file(template_features, '$output_file')
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21 ]]></configfile>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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22 </configfiles>
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38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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24 <inputs>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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25 <param name="files" type="data_collection" collection_type="list" format="parquet" label="Input data"
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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26 help="Table containing clustered features." />
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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27 </inputs>
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29 <outputs>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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30 <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" />
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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31 </outputs>
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38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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33 <tests>
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38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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35 </tests>
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37 <help>
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38 <![CDATA[
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39 @COMPUTE_TEMPLATE_HELP@
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41 @GENERAL_HELP@
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43 ]]>
38469e025939 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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44 </help>
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46 <expand macro="citations"/>
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47 </tool>