Mercurial > repos > mvdbeek > damidseq_average_scores
view average_scores.xml @ 0:427f5dda8854 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_average_score commit 3f1b0838d9fd6256d61490c3b2b52936b9ce2123
author | mvdbeek |
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date | Fri, 27 Apr 2018 14:54:05 -0400 |
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children | 7fd65542efc2 |
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<tool id="average_score" name="Calculate average scores" version="0.1.3"> <description>for fixed step interval files</description> <requirements> <requirement type="package" version="0.22">pandas</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$average_script' ]]></command> <configfiles> <configfile name="average_script"> import pandas as pd #set files = [str(f) for f in $input_files] #set column = 3 if $input_files[0].ext in ['bed', 'bedgraph'] else 5 d = {} #for f in $files: d['$f'] = pd.read_csv('$f', usecols=[$column], sep="\t", skiprows=$skiprows, header=None, squeeze=True) #end for df = pd.DataFrame.from_dict(d) mean = df.mean(axis=1) with open('$averaged_output', 'w') as out, open('$files[0]') as first_file: for i, line in enumerate(first_file): fields = line.strip().split("\t") if i >= $skiprows: fields[$column] = str(mean[i - $skiprows]) out.write("%s\n" % "\t".join(fields)) </configfile> </configfiles> <inputs> <param name="input_files" type="data" multiple="true" format="bed,bedgraph,gff" label="Select the files for which to average the score"/> <param name="skiprows" type="integer" min="0" value="0" label="Skip the first N rows" help="To skip comments and track definition lines"/> </inputs> <outputs> <data name="averaged_output" format_source="input_files" label="${tool.name} on ${on_string}"/> </outputs> <tests> <test> <param name="input_files" value="1.bed,2.bed" ftype="bed"/> <output name="averaged_output" value="averaged.bed" ftype="bed"/> </test> </tests> <help><![CDATA[ What it does ------------ This tool calculates the average value for the score column across many datasets. ]]></help> </tool>