1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/72ed536a988d/ changeset: 72ed536a988d user: dan date: 2011-09-23 19:49:33 summary: Rewrite random lines tool. Does two passes through input file: first pass determines line offsets/count, offsets are randomly removed, second pass writes out lines by seeking to remaining offsets. The random seed can now be optionally specified. affected #: 3 files (-1 bytes)

--- a/tools/filters/randomlines.xml Fri Sep 23 13:26:34 2011 -0400 +++ b/tools/filters/randomlines.xml Fri Sep 23 13:49:33 2011 -0400 @@ -1,9 +1,25 @@ -<tool id="random_lines1" name="Select random lines"> +<tool id="random_lines1" name="Select random lines" version="2.0.0"><description>from a file</description> - <command interpreter="python">randomlines.py $input $num_lines $out_file1</command> + <command interpreter="python">random_lines_two_pass.py "${input}" "${out_file1}" "${num_lines}" + #if str( $seed_source.seed_source_selector ) == "set_seed": + --seed "${seed_source.seed}" + #end if + </command><inputs><param name="num_lines" size="5" type="integer" value="1" label="Randomly select" help="lines"/><param format="txt" name="input" type="data" label="from"/> + <conditional name="seed_source"> + <param name="seed_source_selector" type="select" label="Set a random seed"> + <option value="no_seed" selected="True">Don't set seed</option> + <option value="set_seed">Set seed</option> + </param> + <when value="no_seed"> + <!-- Do nothing here --> + </when> + <when value="set_seed"> + <param name="seed" type="text" label="Random seed" /> + </when> + </conditional></inputs><outputs><data format="input" name="out_file1" metadata_source="input"/> @@ -12,8 +28,16 @@ <test><param name="num_lines" value="65"/><param name="input" value="1.bed"/> + <param name="seed_source_selector" value="no_seed"/><output name="out_file1" file="1.bed"/></test> + <test> + <param name="num_lines" value="1"/> + <param name="input" value="1.bed"/> + <param name="seed_source_selector" value="set_seed"/> + <param name="seed" value="asdf"/> + <output name="out_file1" file="1_bed_random_lines_1_seed_asdf_out.bed"/> + </test></tests><help>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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