Mercurial > repos > mvdbeek > damidseq_average_scores

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
author mvdbeek
date Sat, 28 Apr 2018 13:51:18 -0400
parents 427f5dda8854
children
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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
parents:
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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
parents:
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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 $input_files]
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7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
parents: 0
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14 #set column = {'bed': 4, 'bedgraph': 3, 'gff': 5, 'gff3': 5, 'gtf': 5}[$input_files[0].ext]
7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
parents: 0
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15 skiprows = 0
7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
parents: 0
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16 with open('$files[0]') as first_file:
7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
parents: 0
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17 for i, line in enumerate(first_file):
7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
parents: 0
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18 if not line.startswith(('track', 'browser', '#')):
7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
parents: 0
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19 skiprows = i
7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
parents: 0
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20 break
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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 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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22 #for f in $files:
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7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
parents: 0
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23 d['$f'] = pd.read_csv('$f', usecols=[$column], sep="\t", skiprows=skiprows, header=None, squeeze=True)
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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 #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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25 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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26 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
parents:
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27 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
parents:
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28 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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29 fields = line.strip().split("\t")
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7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
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30 if i >= skiprows:
7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
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31 fields[$column] = str(mean[i - skiprows])
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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 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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33 </configfile>
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 </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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35 <inputs>
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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36 <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
parents:
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37 </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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38 <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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39 <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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40 </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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41 <tests>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
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42 <test>
1
7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
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43 <param name="input_files" value="1.bed,2.bed" ftype="bedgraph"/>
7fd65542efc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 14ffe107199084dcb9f4a9f693ef7b6be097a87b
mvdbeek
parents: 0
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44 <output name="averaged_output" value="averaged.bed" ftype="bedgraph"/>
0
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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45 </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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46 </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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47 <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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48 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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49 ------------
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
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50
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
mvdbeek
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51 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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52
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
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53 ]]></help>
427f5dda8854 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
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54 </tool>