annotate FilterTableByNamesList.xml @ 0:f92e6aff30b7 default tip

initial commit

<?xml version="1.0"?>

<tool id="filter_by_list_1" name="Filter a tabular file">
  <description>against a list of desired column values</description>
  <version_string>echo 1.0.0</version_string>
  <command interpreter="perl">filter_by_list $case_sensitive $input_table $file_of_names $filtered_output_table $num_header_lines</command>
  <inputs>
    <param format="tabular" name="input_table" type="data" label="Text table to filter"/>
    <param format="text" name="file_of_names" type="data" label="Text file with target names" help="Input lines with any of these names in any column will be retained"/>
    <param name="case_sensitive" type="boolean" value="True" label="Case sensitive?"/>
    <param name="num_header_lines" type="integer" value="1" min="-1" max="100" label="Number of header lines" help="These will be copied to the output verbatim, without checking for names match. Specifying -1 will copy all lines starting with a pound sign (#)"/>
  </inputs>
  <outputs>
    <data name="filtered_output_table" format="tabular" type="data" label="Subset of table matching specific names"/>
  </outputs>

  <tests/>

  <help>
This tool retains lines of an  input tabular file that have a column value matching any of the values in the "names" file. This is useful for example to 
report only a subset of an HGVS or BED file corresponding to a set of genes of interest. The names file should have one name per line. If you are looking to
only match one name, it might be just as easy to use the generic Galaxy tool "Select lines that match an expression". 
 </help>

</tool>