Mercurial > repos > mvdbeek > damidseq_average_scores

annotate average_scores.xml @ 0:427f5dda8854 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
author mvdbeek
date Fri, 27 Apr 2018 14:54:05 -0400
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children 7fd65542efc2
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427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
parents:
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1 <tool id="average_score" name="Calculate average scores" version="0.1.3">
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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2 <description>for fixed step interval files</description>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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3 <requirements>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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4 <requirement type="package" version="0.22">pandas</requirement>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
parents:
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5 </requirements>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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6 <command detect_errors="exit_code"><![CDATA[
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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7 python '$average_script'
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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8 ]]></command>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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9 <configfiles>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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10 <configfile name="average_script">
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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11 import pandas as pd
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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12
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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13 #set files = [str(f) for f in $input_files]
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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14 #set column = 3 if $input_files[0].ext in ['bed', 'bedgraph'] else 5
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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15 d = {}
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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16 #for f in $files:
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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17 d['$f'] = pd.read_csv('$f', usecols=[$column], sep="\t", skiprows=$skiprows, header=None, squeeze=True)
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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18 #end for
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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19 df = pd.DataFrame.from_dict(d)
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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20 mean = df.mean(axis=1)
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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21 with open('$averaged_output', 'w') as out, open('$files[0]') as first_file:
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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22 for i, line in enumerate(first_file):
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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23 fields = line.strip().split("\t")
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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24 if i >= $skiprows:
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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25 fields[$column] = str(mean[i - $skiprows])
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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26 out.write("%s\n" % "\t".join(fields))
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
parents:
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27 </configfile>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
parents:
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28 </configfiles>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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29 <inputs>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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30 <param name="input_files" type="data" multiple="true" format="bed,bedgraph,gff" label="Select the files for which to average the score"/>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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31 <param name="skiprows" type="integer" min="0" value="0" label="Skip the first N rows" help="To skip comments and track definition lines"/>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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32 </inputs>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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33 <outputs>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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34 <data name="averaged_output" format_source="input_files" label="${tool.name} on ${on_string}"/>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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35 </outputs>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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36 <tests>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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37 <test>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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38 <param name="input_files" value="1.bed,2.bed" ftype="bed"/>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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39 <output name="averaged_output" value="averaged.bed" ftype="bed"/>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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40 </test>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
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41 </tests>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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42 <help><![CDATA[
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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43 What it does
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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44 ------------
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
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45
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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46 This tool calculates the average value for the score column across many datasets.
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
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47
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
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48 ]]></help>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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49 </tool>