Mercurial > repos > recetox > recetox_aplcms_generate_feature_table
annotate recetox_aplcms_generate_feature_table.xml @ 9:b3413f335327 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a
| author | recetox |
|---|---|
| date | Thu, 01 Aug 2024 10:59:05 +0000 |
| parents | 32b66fb6a6a0 |
| children | 89178a72388a |
| rev | line source |
|---|---|
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9
b3413f335327
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a
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1 <tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0" profile="21.09"> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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2 <description>generate feature table from noise-removed HRMS profile data</description> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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3 <macros> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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4 <import>macros.xml</import> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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5 <import>help.xml</import> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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6 </macros> |
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7
32b66fb6a6a0
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 97249a1af94ac5c387e1ede274dec5364f71cde9
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7 <expand macro="annotation"/> |
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5
702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
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8 <edam_operations> |
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702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
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9 <edam_operation>operation_3215</edam_operation> |
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702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
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10 <edam_operation>operation_3799</edam_operation> |
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702a849c1e0e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
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11 </edam_operations> |
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7
32b66fb6a6a0
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 97249a1af94ac5c387e1ede274dec5364f71cde9
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12 <expand macro="refs"/> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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13 <expand macro="creator"/> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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14 <expand macro="requirements"/> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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15 |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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16 <command detect_errors="aggressive"><![CDATA[ |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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17 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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18 ]]></command> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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19 <configfiles> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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20 <configfile name="run_script"><![CDATA[ |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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21 profile <- load_data_from_parquet_file('$profile') |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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22 sample_name <- load_sample_name(profile) |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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23 |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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24 if(is.na(sample_name)) { |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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25 message("The file does not contain sample name.") |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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26 } |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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27 |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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28 feature_table <- prof.to.features( |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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29 profile = profile, |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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30 bandwidth = $bandwidth, |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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31 #if $min_bandwidth: |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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32 min_bandwidth = $min_bandwidth, |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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33 #else: |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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34 min_bandwidth = NA, |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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35 #end if |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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36 #if $max_bandwidth: |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
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37 max_bandwidth = $max_bandwidth, |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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38 #else: |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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39 max_bandwidth = NA, |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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40 #end if |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 0873c036d734782d2647b0eea84cd1a0658f5e58
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41 #if $advanced.sd_cut.sd_cut_bounds == "TRUE": |
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e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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42 sd_cut = c($advanced.sd_cut.sd_cut_min, $advanced.sd_cut.sd_cut_max), |
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e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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43 #else |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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44 sd_cut = c(0, Inf), |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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45 #end if |
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1
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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46 sigma_ratio_lim = determine_sigma_ratios($advanced.shape_model.sigma_ratio_lim_min, $advanced.shape_model.sigma_ratio_lim_max), |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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47 shape_model = "bi-Gaussian", |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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48 peak_estim_method = "$advanced.peak_estim.peak_estim_method", |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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49 component_eliminate = $advanced.component_eliminate, |
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e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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50 #if $advanced.peak_estim.peak_estim_method == "moment": |
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e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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51 moment_power = $advanced.peak_estim.moment_power, |
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e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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52 #else |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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53 moment_power = 1, |
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e8962c8340f4
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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54 #end if |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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55 BIC_factor = $BIC_factor, |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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56 do.plot = FALSE |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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57 ) |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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58 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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59 feature_table <- save_sample_name(feature_table, sample_name) |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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60 save_data_as_parquet_file(feature_table, '$output_file') |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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61 ]]></configfile> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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62 </configfiles> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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63 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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64 <inputs> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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65 <param label="Input profile data" name="profile" type="data" format="parquet" |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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66 help="Mass spectrometry profile data." /> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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67 <expand macro="bandwidth_params"/> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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68 <expand macro="generate_feature_table_params"/> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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69 </inputs> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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70 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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71 <outputs> |
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72 <data label="${($profile.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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73 </outputs> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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74 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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75 <tests> |
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7
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76 <test expect_failure="true" /> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 97249a1af94ac5c387e1ede274dec5364f71cde9
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77 <test> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 97249a1af94ac5c387e1ede274dec5364f71cde9
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78 <param name="profile" value="remove_noise_docker.parquet" /> |
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32b66fb6a6a0
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 97249a1af94ac5c387e1ede274dec5364f71cde9
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79 <output name="output_file" file="peak_table_galaxy.parquet" /> |
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32b66fb6a6a0
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 97249a1af94ac5c387e1ede274dec5364f71cde9
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80 </test> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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81 </tests> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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82 |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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83 <help> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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84 <![CDATA[ |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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85 @GENERATE_FEATURE_TABLE_HELP@ |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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86 |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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87 @GENERAL_HELP@ |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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88 ]]> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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89 </help> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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90 |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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91 <expand macro="citations"/> |
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2810c956ec39
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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92 </tool> |