Mercurial > repos > bgruening > split_file_on_column
view split_file_on_column.xml @ 3:b60f2452580e draft
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author | bgruening |
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date | Wed, 23 Dec 2015 03:50:48 -0500 |
parents | 90b52d8d6f2c |
children | 37a53100b67e |
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<tool id="tp_split_on_column" name="Split file" version="0.2"> <description>according to the values of a column</description> <requirements> <requirement type="package" version="4.1.0">gnu_awk</requirement> </requirements> <command> <![CDATA[ mkdir tmp_out && awk -F'\t' '{print > "tmp_out/"\$$column".$infile.ext" }' $infile ]]> </command> <inputs> <param format="tabular" name="infile" type="data" label="File to select" /> <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" /> </inputs> <outputs> <collection name="split_output" type="list" label="Table split on first column"> <discover_datasets pattern="__name_and_ext__" directory="tmp_out" /> </collection> </outputs> <tests> <test> <param name="infile" value="5cols.tabular" ftype="tabular"/> <param name="column" value="5" /> <output_collection name="split_output" type="list"> <element name="1"> <assert_contents> <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" /> </assert_contents> </element> <element name="2"> <assert_contents> <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" /> </assert_contents> </element> </output_collection> </test> </tests> <help> <![CDATA[ **What it does** This tool splits a file into different smaller files using a specific column. It will work like the group tool, but every group is saved to its own file. ----- **Example** Splitting on column 5 from this:: chr7 56632 56652 cluster 1 chr7 56736 56756 cluster 1 chr7 56761 56781 cluster 2 chr7 56772 56792 cluster 2 chr7 56775 56795 cluster 2 will produce 2 files with different clusters:: chr7 56632 56652 cluster 1 chr7 56736 56756 cluster 1 chr7 56761 56781 cluster 2 chr7 56772 56792 cluster 2 chr7 56775 56795 cluster 2 ]]> </help> </tool>