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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>
tools/encode/random_intervals.xml
+3 -2
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@@ -1,6 +1,6 @@
<tool id="random_intervals1" name="Random Intervals">
<description>create a random set of intervals</description>
<command interpreter="python">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 $input2_chromCol $input2_startCol $input2_endCol $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol $use_mask $strand_overlaps ${GALAXY_DATA_INDEX_DIR}</command>
<command interpreter="python">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 ${input2.metadata.chromCol} ${input2.metadata.startCol} ${input2.metadata.endCol} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} $use_mask $strand_overlaps ${GALAXY_DATA_INDEX_DIR}</command>
<inputs>
<param name="input1" type="data" format="interval" label="File to Mimick">
<validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16 or hg17. Click the pencil icon in your history item to set the genome build."/>
@@ -21,6 +21,7 @@
<column name="value" index="1"/>
<column name="dbkey" index="0"/>
<filter type="data_meta" ref="input1" key="dbkey" column="0" />
<validator type="no_options" message="This tool currently only works with ENCODE data from genome builds hg16 or hg17."/>
</options>
</param>
</inputs>
@@ -31,7 +32,7 @@
.. class:: warningmark
This tool currently only works with data from genome builds hg16 or hg17.
This tool currently only works with ENCODE data from genome builds hg16 or hg17.
-----
tools/encode/split_by_partitions.py
+1 -1
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@@ -57,7 +57,7 @@ def main():
try:
strandCol = int( sys.argv[7] )-1
except:
stop_err( "Bad strand column: %s" % ( str( sys.argv[7] ) ) )
strandCol = -1
line_count = 0
skipped_lines = 0