diff FilterTableByNamesList.xml @ 0:f92e6aff30b7 default tip

initial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FilterTableByNamesList.xml	Wed Mar 25 13:35:07 2015 -0600
@@ -0,0 +1,25 @@
+<?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>