Mercurial > repos > devteam > column_maker
view column_maker.xml @ 4:3335c0d583d8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 2b17bdfc47ca4d7f1a584216c4bd61a7050df7ea"
author | devteam |
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date | Thu, 04 Jun 2020 09:03:25 +0000 |
parents | 35937a6b04fb |
children | c6fdc1118036 |
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<tool id="Add_a_column1" name="Compute" version="1.3.0"> <description>an expression on every row</description> <requirements> <requirement type="package" version="2.7.13">python</requirement> <requirement type="package" version="4.4">sed</requirement> <requirement type="package" version="1.14">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 python '$__tool_directory__/column_maker.py' data column_maker_output "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}" $avoid_scientific_notation && cat header column_maker_output > '$out_file1' ]]></command> <inputs> <param name="cond" type="text" value="c3-c2" label="Add expression"/> <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> <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> <when value="no"> </when> <when value="yes"> <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"/> </outputs> <tests> <test> <param name="cond" value="c3-c2"/> <param name="input" value="1.bed"/> <param name="round" value="no"/> <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"/> <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"/> <conditional name="header_lines_conditional"> <param name="header_lines_select" value="yes" /> <param name="header_new_column_name" value="value1_again" /> </conditional> <output name="out_file1" file="column_maker_out2.header.tsv"/> </test> <test> <param name="cond" value="c4*1"/> <param name="input" value="1.interval"/> <param name="round" value="yes"/> <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"/> <output name="out_file1"> <assert_contents> <has_text text="CCDS10397" /> <has_text text="1e-13" /> </assert_contents> </output> </test> <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"/> <output name="out_file1"> <assert_contents> <has_text text="CCDS10397" /> <has_text text=".0000000000001" /> <not_has_text text="1e-13" /> </assert_contents> </output> </test> </tests> <help> .. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* ----- **What it does** This tool computes an expression for every row of a dataset and appends the result as a new column (field). - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file - **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position ----- **Example** If this is your input:: chr1 151077881 151077918 2 200 - chr1 151081985 151082078 3 500 + computing "c4*c5" will produce:: chr1 151077881 151077918 2 200 - 400.0 chr1 151081985 151082078 3 500 + 1500.0 if, at the same time, "Round result?" is set to **YES** results will look like this:: chr1 151077881 151077918 2 200 - 400 chr1 151081985 151082078 3 500 + 1500 You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following:: chr1 151077881 151077918 2 200 - True chr1 151081985 151082078 3 500 + True or computing "type(c2)==type('') for Input will return:: chr1 151077881 151077918 2 200 - False chr1 151081985 151082078 3 500 + False The following build-in functions are available:: abs | all | any | bin | bool | chr | ceil | cmp | complex divmod | exp | float | log | floor | hex | int | len | long max | min | oct | ord | pow | range | reversed round | sorted | sqrt | str | sum | type | unichr | unicode | </help> <citations /> </tool>