Mercurial > repos > mvdbeek > add_input_name_as_column
changeset 5:06061aa49527 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
| author | mvdbeek |
|---|---|
| date | Wed, 06 Mar 2019 09:16:29 -0500 |
| parents | b31219f26a8f |
| children | 3284b72eef56 |
| files | add_input_name_as_column.py add_input_name_as_column.xml tool |
| diffstat | 3 files changed, 37 insertions(+), 33 deletions(-) [+] |
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--- a/add_input_name_as_column.py Fri Mar 20 14:51:56 2015 +0100 +++ b/add_input_name_as_column.py Wed Mar 06 09:16:29 2019 -0500 @@ -1,25 +1,25 @@ -import sys +import io import argparse + def Parser(): - the_parser = argparse.ArgumentParser(description="add label to last column of file") - the_parser.add_argument('--input', required=True, action="store", type=str, help="input tabular file") - the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path") - the_parser.add_argument('--label', required=True, action="store", type=str, help="label to add in last column") - the_parser.add_argument('--header', action="store", type=str, help="column label for last column") - args = the_parser.parse_args() - return args + the_parser = argparse.ArgumentParser(description="add label to last column of file") + the_parser.add_argument('--input', required=True, action="store", type=str, help="input tabular file") + the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path") + the_parser.add_argument('--label', required=True, action="store", type=str, help="label to add in last column") + the_parser.add_argument('--header', action="store", type=str, help="column label for last column") + args = the_parser.parse_args() + return args -args=Parser() -input=open(args.input) -output=open(args.output, 'w') -for i,line in enumerate(input): - line=line.strip('\n') - if (i==0) and (args.header!=None): - line=line+'\t'+args.header - else: - line=line+'\t'+args.label - print >>output, line -input.close() -output.close() +args = Parser() + + +with io.open(args.input, encoding="utf-8") as input, io.open(args.output, 'w', encoding="utf-8") as output: + for i, line in enumerate(input): + line = line.strip('\n') + if (i == 0) and args.header: + line = "%s\t%s\n" % (line, args.header) + else: + line = "%s\t%s\n" % (line, args.label) + output.write(line)
--- a/add_input_name_as_column.xml Fri Mar 20 14:51:56 2015 +0100 +++ b/add_input_name_as_column.xml Wed Mar 06 09:16:29 2019 -0500 @@ -1,26 +1,30 @@ -<tool id="addName" name="Add input name as column" version="0.1.1"> +<tool id="addName" name="Add input name as column" version="0.1.2" profile="17.09"> <description>to an existing tabular file</description> - <command interpreter="python">add_input_name_as_column.py - --input "$input" - --label "$input.element_identifier" - --output "$output" - #if $header.contains_header=="yes": - --header "$header.colname" - #end if - </command> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> + <command><![CDATA[ +python '$__tool_directory__/'add_input_name_as_column.py +--input '$input' +--label '$input.element_identifier' +--output '$output' +#if $header.contains_header=="yes": + --header "$header.colname" +#end if + ]]></command> <inputs> - <param format="tabular" name="input" type="data" label="to Dataset" help="Dataset missing? See TIP below" /> + <param format="txt" name="input" type="data" label="to Dataset" help="Dataset missing? See TIP below" /> <conditional name="header"> <param name="contains_header" type="select" label="input contains a header line?" > <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> - <when value="yes"> + <when value="yes"> <param name="colname" type="text" value="sample" help="select a column header to be added in the first line"> <validator type="empty_field" message="please add a column header"/> </param> </when> - <when value="no"> + <when value="no"> </when> </conditional> </inputs> @@ -51,7 +55,7 @@ **What it does** Adds a new column with the name of the input file as it appears in the history. -Written by Marius van den Beek, m.vandenbeek at gmail . com +Written by Marius van den Beek, m.vandenbeek at gmail dot com </help> </tool>