Mercurial > repos > devteam > column_maker
diff column_maker.xml @ 6:13b6f0007d9e draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
| author | devteam |
|---|---|
| date | Mon, 25 Jan 2021 10:00:12 +0000 |
| parents | 9cd341095afd |
| children | 427903d47026 |
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--- a/column_maker.xml Wed Dec 30 00:50:15 2020 +0000 +++ b/column_maker.xml Mon Jan 25 10:00:12 2021 +0000 @@ -1,45 +1,52 @@ -<tool id="Add_a_column1" name="Compute" version="1.4"> +<tool id="Add_a_column1" name="Compute" version="1.5"> <description>an expression on every row</description> <requirements> <requirement type="package" version="3.8">python</requirement> - <requirement type="package" version="4.4">sed</requirement> <requirement type="package" version="1.19.1">numpy</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ - #if $header_lines_conditional.header_lines_select == "yes": - (sed -n '1,1p' '$input' | sed "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header && - sed '1,1d' '$input' > data && - #else: - touch header && - ln -s '$input' data && - #end if + ln -s '$input' data && ## inject colums and column_types metadata into inputs json #import json #set inputs_dict = json.load(open($inputs)) #set inputs_dict['columns'] = $input.metadata.columns #set inputs_dict['column_types'] = $input.metadata.column_types + ## flatten conditional + #if $header_lines_conditional.header_lines_select == "yes": + #set inputs_dict['header_new_column_name'] = str($header_lines_conditional.header_new_column_name) + #end if #set x = json.dump($inputs_dict, open($inputs, 'w')) python '$__tool_directory__/column_maker.py' - data column_maker_output + data '$out_file1' --load_json '$inputs' - && cat header column_maker_output > '$out_file1' ]]></command> <configfiles> <inputs name="inputs"/> </configfiles> <inputs> - <param name="cond" type="text" value="c3-c2" label="Add expression"/> + <param name="cond" type="text" value="c3-c2" label="Add expression"> + <sanitizer> + <valid initial="default"> + <add value="<" /> + <add value=">" /> + <add value=""" /> + <add value="'" /> + </valid> + </sanitizer> + </param> <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/> - <param name="round" type="select" label="Round result?"> - <option value="no">NO</option> - <option value="yes">YES</option> - </param> + <param name="round" type="boolean" truevalue="yes" falsevalue="no" label="Round result?" /> + <param name="avoid_scientific_notation" type="boolean" truevalue="yes" falsevalue="no" + label="Avoid scientific notation" + help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers)." /> <conditional name="header_lines_conditional"> - <param name="header_lines_select" type="select" label="Skip a header line" help="# characters are already considered as comments and kept" > - <option value="no" >no</option> - <option value="yes" >yes</option> + <param name="header_lines_select" type="select" + label="Input has a header line with column names?" + help="Select Yes to be able to specify a name for the new column and have it added to the header line. If you select No, the first line will be treated as a regular line: If it is empty or starts with a # character it will be skipped, otherwise the tool will attempt to compute the specified expression on it." > + <option value="no" >No</option> + <option value="yes" >Yes</option> </param> <when value="no"> </when> @@ -47,10 +54,6 @@ <param name="header_new_column_name" type="text" value="New Column" label="The new column name" /> </when> </conditional> - <param name="avoid_scientific_notation" type="select" label="Avoid scientific notation" help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers)."> - <option value="no">no</option> - <option value="yes">yes</option> - </param> </inputs> <outputs> <data format_source="input" name="out_file1" metadata_source="input"/> @@ -59,19 +62,19 @@ <test> <param name="cond" value="c3-c2"/> <param name="input" value="1.bed"/> - <param name="round" value="no"/> + <param name="round" value="false"/> <output name="out_file1" file="column_maker_out1.interval"/> </test> <test> <param name="cond" value="c4*1"/> <param name="input" value="1.interval"/> - <param name="round" value="no"/> + <param name="round" value="false"/> <output name="out_file1" file="column_maker_out2.interval"/> </test> <test> <param name="cond" value="c4*1"/> <param name="input" value="1.header.tsv"/> - <param name="round" value="no"/> + <param name="round" value="false"/> <conditional name="header_lines_conditional"> <param name="header_lines_select" value="yes" /> <param name="header_new_column_name" value="value1_again" /> @@ -81,13 +84,13 @@ <test> <param name="cond" value="c4*1"/> <param name="input" value="1.interval"/> - <param name="round" value="yes"/> + <param name="round" value="true"/> <output name="out_file1" file="column_maker_out3.interval"/> </test> <test> <param name="cond" value="float(.0000000000001)"/> <param name="input" value="1.bed"/> - <param name="round" value="no"/> + <param name="round" value="false"/> <output name="out_file1"> <assert_contents> <has_text text="CCDS10397" /> @@ -98,8 +101,8 @@ <test> <param name="cond" value="float(.0000000000001)"/> <param name="input" value="1.bed"/> - <param name="round" value="no"/> - <param name="avoid_scientific_notation" value="yes"/> + <param name="round" value="false"/> + <param name="avoid_scientific_notation" value="true"/> <output name="out_file1"> <assert_contents> <has_text text="CCDS10397" />