Mercurial > repos > mvdbeek > damidseq_average_scores
changeset 0:427f5dda8854 draft
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 |
| parents | |
| children | 7fd65542efc2 |
| files | average_scores.xml test-data/1.bed test-data/2.bed test-data/averaged.bed |
| diffstat | 4 files changed, 109 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/average_scores.xml Fri Apr 27 14:54:05 2018 -0400 @@ -0,0 +1,49 @@ +<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>
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