Mercurial > repos > devteam > column_maker
diff column_maker.xml @ 3:35937a6b04fb draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit f6e96ffa420035051ea4632596dfd171074aa66d
author | devteam |
---|---|
date | Thu, 25 Oct 2018 17:31:05 -0400 |
parents | 292c605c2dc7 |
children | 3335c0d583d8 |
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--- a/column_maker.xml Fri Dec 18 18:52:53 2015 -0500 +++ b/column_maker.xml Thu Oct 25 17:31:05 2018 -0400 @@ -1,40 +1,79 @@ -<tool id="Add_a_column1" name="Compute" version="1.1.0"> - <description>an expression on every row</description> - <command interpreter="python"> - column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}" - </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> - </inputs> - <outputs> - <data format="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.interval"/> - <param name="round" value="yes"/> - <output name="out_file1" file="column_maker_out3.interval"/> - </test> - </tests> - <help> +<tool id="Add_a_column1" name="Compute" version="1.2.0"> + <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> + </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}" && + 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> + </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> + </tests> + <help> .. class:: infomark @@ -63,7 +102,7 @@ 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 @@ -90,5 +129,6 @@ round | sorted | sqrt | str | sum | type | unichr | unicode | - </help> + </help> + <citations /> </tool>