Mercurial > repos > saskia-hiltemann > file_manipulation
diff sort_chromosomal_position.xml @ 0:e77c9484b2d0 draft default tip
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author | saskia-hiltemann |
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date | Thu, 22 Oct 2015 09:18:30 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sort_chromosomal_position.xml Thu Oct 22 09:18:30 2015 -0400 @@ -0,0 +1,31 @@ +<tool id="sort_chrom_pos" name="Sort Chromosomal Position" version="1" > + <description> sort file by chromosome, then by position </description> + <command interpreter="bash"> + sort_chromosomal_position.sh $infile $chrcol $startcol $endcol $num_headerlines $sorted_file + </command> + + + <inputs> + + <param name="infile" type="data" label="select file to be sorted" help="must be a tab-separated file with a 1 line header"/> + <param name="chrcol" type="data_column" data_ref="infile" multiple="False" label="Chromosome Column" /> + <param name="startcol" type="data_column" data_ref="infile" multiple="False" label="Start Column" /> + <param name="endcol" type="data_column" data_ref="infile" multiple="False" label="End Column" /> + <param name="num_headerlines" type="text" value="1" label="number of headerlines in your file" help="these lines will not be sorted"/> + + <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/> + </inputs> + + <outputs> + <data format="tabular" name="sorted_file" label="$fname ${tool.name} Annotated region on file ${on_string}"/> + + </outputs> + + <help> + + +</help> + +</tool> + +