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Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.

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Greg Von Kuster
2008-07-23 15:27:39 -04:00
parent 9dbf7c0385
commit 5dd014a91e
30 changed files with 44 additions and 70 deletions
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tools/encode/gencode_partition.xml
+1 -1
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@@ -1,6 +1,6 @@
<tool id="gencode_partition1" name="Gencode Partition">
<description>an interval file</description>
<command interpreter="python">split_by_partitions.py /home/universe/encode_feature_partitions/partition_list.txt $input1 $out_file1 $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol</command>
<command interpreter="python">split_by_partitions.py /home/universe/encode_feature_partitions/partition_list.txt $input1 $out_file1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command>
<inputs>
<param name="input1" type="data" format="interval" label="File to Partition"/>
</inputs>