Mercurial > repos > devteam > cut_columns
changeset 1:f848742a0c1a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
| author | devteam |
|---|---|
| date | Fri, 05 Aug 2016 16:37:57 -0400 |
| parents | aa367513335f |
| children | |
| files | cutWrapper.pl cutWrapper.xml |
| diffstat | 2 files changed, 229 insertions(+), 202 deletions(-) [+] |
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--- a/cutWrapper.pl Mon Nov 09 11:28:29 2015 -0500 +++ b/cutWrapper.pl Fri Aug 05 16:37:57 2016 -0400 @@ -9,6 +9,9 @@ my @out = (); my $command = ""; my $field = 0; +my $start = 0; +my $end = 0; +my $i = 0; # a wrapper for cut for use in galaxy # cutWrapper.pl [filename] [columns] [delim] [output] @@ -20,6 +23,13 @@ if (m/^c\d{1,}$/i) { push (@columns, $_); $columns[@columns-1] =~s/c//ig; + } elsif (m/^c\d{1,}-c\d{1,}$/i) { + ($start, $end) = split(/-/, $_); + $start =~ s/c//ig; + $end =~ s/c//ig; + for $i ($start .. $end) { + push (@columns, $i); + } } }
--- a/cutWrapper.xml Mon Nov 09 11:28:29 2015 -0500 +++ b/cutWrapper.xml Fri Aug 05 16:37:57 2016 -0400 @@ -1,202 +1,219 @@ -<tool id="Cut1" name="Cut" version="1.0.1"> - <description>columns from a table</description> - <command interpreter="perl">cutWrapper.pl "${input}" "${columnList}" "${delimiter}" "${out_file1}"</command> - <inputs> - <param name="columnList" type="text" value="c1,c2" label="Cut columns"/> - <param name="delimiter" type="select" label="Delimited by"> - <option value="T">Tab</option> - <option value="Sp">Whitespace</option> - <option value="Dt">Dot</option> - <option value="C">Comma</option> - <option value="D">Dash</option> - <option value="U">Underscore</option> - <option value="P">Pipe</option> - </param> - <param format="txt" name="input" type="data" label="From"/> - </inputs> - <outputs> - <data format="tabular" name="out_file1" > - <actions> - <conditional name="delimiter"> - <when value="T"> - <conditional name="input"> - <when datatype_isinstance="interval"> - <action type="format" default="tabular"> - <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 1--> - - <filter type="insert_column" column="0" value="interval"/> - - <filter type="insert_column" ref="columnList" /> <!-- startCol --> - - <filter type="insert_column" ref="columnList" /> <!-- endCol --> - - <filter type="multiple_splitter" column="1" separator=","/> - <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="1" name="lower" /> - <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's --> - <filter type="boolean" column="1" cast="int" /> - - <filter type="multiple_splitter" column="2" separator=","/> - <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="2" name="lower" /> - <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's --> - <filter type="boolean" column="2" cast="int" /> - - <filter type="multiple_splitter" column="3" separator=","/> - <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="3" name="lower" /> - <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's --> - <filter type="boolean" column="3" cast="int" /> - - <filter type="metadata_value" ref="input" name="chromCol" column="1" /> - <filter type="metadata_value" ref="input" name="startCol" column="2" /> - <filter type="metadata_value" ref="input" name="endCol" column="3" /> - - </option> - </action> - - <conditional name="out_file1"> - <when datatype_isinstance="interval"> - <action type="metadata" name="chromCol"> - <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="chromCol" column="1" /> - </option> - </action> - - <action type="metadata" name="startCol"> - <option type="from_param" name="columnList" column="0" offset="0"> <!-- startCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="startCol" column="1" /> - </option> - </action> - - <action type="metadata" name="endCol"> - <option type="from_param" name="columnList" column="0" offset="0"> <!-- endCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="endCol" column="1" /> - </option> - </action> - - <action type="metadata" name="nameCol" default="0"> - <option type="from_param" name="columnList" column="0" offset="0"> <!-- nameCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="nameCol" column="1" /> - </option> - </action> - - <action type="metadata" name="strandCol" default="0"> - <option type="from_param" name="columnList" column="0" offset="0"> <!-- strandCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="strandCol" column="1" /> - </option> - </action> - </when> - </conditional> - - </when> - </conditional> - </when> - </conditional> - </actions> - </data> - </outputs> - <tests> - <test> - <param name="columnList" value="c1,c4,c2,c3"/> - <param name="delimiter" value="T"/> - <param name="input" value="1.bed"/> - <output name="out_file1" file="eq-cut.dat"/> - </test> - </tests> - <help> - -.. class:: warningmark - -**WARNING: This tool breaks column assignments.** To re-establish column assignments run the tools and click on the pencil icon in the latest history item. - -.. class:: infomark - -The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example: - - Cutting columns 1 and 3 from:: - - apple,is,good - windows,is,bad - - will give:: - - apple good - windows bad - ------ - -**What it does** - -This tool selects (cuts out) specified columns from the dataset. - -- Columns are specified as **c1**, **c2**, and so on. Column count begins with **1** -- Columns can be specified in any order (e.g., **c2,c1,c6**) -- If you specify more columns than actually present - empty spaces will be filled with dots - ------ - -**Example** - -Input dataset (six columns: c1, c2, c3, c4, c5, and c6):: - - chr1 10 1000 gene1 0 + - chr2 100 1500 gene2 0 + - -**cut** on columns "**c1,c4,c6**" will return:: - - chr1 gene1 + - chr2 gene2 + - -**cut** on columns "**c6,c5,c4,c1**" will return:: - - + 0 gene1 chr1 - + 0 gene2 chr2 - - -**cut** on columns "**c8,c7,c4**" will return:: - - . . gene1 - . . gene2 - - -</help> -</tool> +<tool id="Cut1" name="Cut" version="1.0.2"> + <description>columns from a table</description> + <command> + perl $__tool_directory__/cutWrapper.pl + "${input}" + "${columnList}" + "${delimiter}" + "${out_file1}" + </command> + <inputs> + <param name="columnList" type="text" value="c1,c2" label="Cut columns"/> + <param name="delimiter" type="select" label="Delimited by"> + <option value="T">Tab</option> + <option value="Sp">Whitespace</option> + <option value="Dt">Dot</option> + <option value="C">Comma</option> + <option value="D">Dash</option> + <option value="U">Underscore</option> + <option value="P">Pipe</option> + </param> + <param format="txt" name="input" type="data" label="From"/> + </inputs> + <outputs> + <data format="tabular" name="out_file1" > + <actions> + <conditional name="delimiter"> + <when value="T"> + <conditional name="input"> + <when datatype_isinstance="interval"> + <action type="format" default="tabular"> + <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 1--> + + <filter type="insert_column" column="0" value="interval"/> + + <filter type="insert_column" ref="columnList" /> <!-- startCol --> + + <filter type="insert_column" ref="columnList" /> <!-- endCol --> + + <filter type="multiple_splitter" column="1" separator=","/> + <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="1" name="lower" /> + <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's --> + <filter type="boolean" column="1" cast="int" /> + + <filter type="multiple_splitter" column="2" separator=","/> + <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="2" name="lower" /> + <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's --> + <filter type="boolean" column="2" cast="int" /> + + <filter type="multiple_splitter" column="3" separator=","/> + <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="3" name="lower" /> + <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's --> + <filter type="boolean" column="3" cast="int" /> + + <filter type="metadata_value" ref="input" name="chromCol" column="1" /> + <filter type="metadata_value" ref="input" name="startCol" column="2" /> + <filter type="metadata_value" ref="input" name="endCol" column="3" /> + + </option> + </action> + + <conditional name="out_file1"> + <when datatype_isinstance="interval"> + <action type="metadata" name="chromCol"> + <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="chromCol" column="1" /> + </option> + </action> + + <action type="metadata" name="startCol"> + <option type="from_param" name="columnList" column="0" offset="0"> <!-- startCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="startCol" column="1" /> + </option> + </action> + + <action type="metadata" name="endCol"> + <option type="from_param" name="columnList" column="0" offset="0"> <!-- endCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="endCol" column="1" /> + </option> + </action> + + <action type="metadata" name="nameCol" default="0"> + <option type="from_param" name="columnList" column="0" offset="0"> <!-- nameCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="nameCol" column="1" /> + </option> + </action> + + <action type="metadata" name="strandCol" default="0"> + <option type="from_param" name="columnList" column="0" offset="0"> <!-- strandCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="strandCol" column="1" /> + </option> + </action> + </when> + </conditional> + + </when> + </conditional> + </when> + </conditional> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="columnList" value="c1,c4,c2,c3"/> + <param name="delimiter" value="T"/> + <param name="input" value="1.bed"/> + <output name="out_file1" file="eq-cut.dat"/> + </test> + <test> + <param name="columnList" value="c1,c4,c2-c3" /> + <param name="delimiter" value="T" /> + <param name="input" value="1.bed" /> + <output name="out_file1" file="eq-cut.dat" /> + </test> + </tests> + <help> + +.. class:: warningmark + +**WARNING: This tool breaks column assignments.** To re-establish column assignments run the tools and click on the pencil icon in the latest history item. + +.. class:: infomark + +The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example: + + Cutting columns 1 and 3 from:: + + apple,is,good + windows,is,bad + linux,is,best + + will give:: + + apple good + windows bad + linux best + +----- + +**What it does** + +This tool selects (cuts out) specified columns from the dataset. + +- Columns are specified as **c1**, **c2**, and so on. Column count begins with **1** +- Columns can be specified in any order (e.g., **c2,c1,c6**) +- If you specify more columns than actually present - empty spaces will be filled with dots + +----- + +**Example** + +Input dataset (six columns: c1, c2, c3, c4, c5, and c6):: + + chr1 10 1000 gene1 0 + + chr2 100 1500 gene2 0 + + +**cut** on columns "**c1,c4,c6**" will return:: + + chr1 gene1 + + chr2 gene2 + + +**cut** on columns "**c6,c5,c4,c1**" will return:: + + + 0 gene1 chr1 + + 0 gene2 chr2 + +**cut** on columns "**c1-c3**" will return:: + + chr1 10 1000 + chr2 100 1500 + + +**cut** on columns "**c8,c7,c4**" will return:: + + . . gene1 + . . gene2 +</help> +</tool>