Mercurial > repos > devteam > weightedaverage
diff WeightedAverage.xml @ 2:efa2b391e887 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
author | devteam |
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date | Wed, 05 Oct 2016 13:39:38 -0400 |
parents | 90611e86a998 |
children |
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--- a/WeightedAverage.xml Thu Apr 03 09:34:41 2014 -0400 +++ b/WeightedAverage.xml Wed Oct 05 13:39:38 2016 -0400 @@ -1,14 +1,15 @@ -<tool id="wtavg" name="Assign weighted-average" version="1.0.0"> +<tool id="wtavg" name="Assign weighted-average" version="1.0.1"> <description> of the values of features overlapping an interval </description> <requirements> <requirement type="package" version="1.0.0">galaxy-ops</requirement> <requirement type="package" version="0.7.1">bx-python</requirement> </requirements> - <command interpreter="python">WeightedAverage.py $genomic_interval $genomic_feature $out_file1 -1 ${genomic_interval.metadata.chromCol},${genomic_interval.metadata.startCol},${genomic_interval.metadata.endCol},${genomic_interval.metadata.strandCol} -2 ${genomic_feature.metadata.chromCol},${genomic_feature.metadata.startCol},${genomic_feature.metadata.endCol},${genomic_feature.metadata.strandCol},${genomic_feature.metadata.nameCol}</command> + <command interpreter="python">WeightedAverage.py $genomic_interval $genomic_feature $out_file1 -1 ${genomic_interval.metadata.chromCol},${genomic_interval.metadata.startCol},${genomic_interval.metadata.endCol},${genomic_interval.metadata.strandCol} -2 ${genomic_feature.metadata.chromCol},${genomic_feature.metadata.startCol},${genomic_feature.metadata.endCol},${genomic_feature.metadata.strandCol},${genomic_feature.metadata.nameCol} ${allow_zeros}</command> <inputs> <param format="interval" name="genomic_interval" type="data" label="Genomic intervals (first dataset)" help="Dataset missing? See Note below."/> <param format="interval" name="genomic_feature" label="Genomic features (second dataset)" type="data" help="Make sure the value column is specified. See Note below." /> + <param name="allow_zeros" label="Include zeros in calculations" type="boolean" help="Otherwise, skip them as bad values" truevalue="--allow_zeros" falsevalue="" checked="True" /> </inputs> <outputs> <data format="input" name="out_file1" metadata_source="genomic_interval" /> @@ -18,9 +19,15 @@ <test> <param name="genomic_interval" value="interval_interpolate.bed"/> <param name="genomic_feature" value="value_interpolate.bed"/> + <param name="allow_zeros" value="False" /> <output name="out_file1" file="interpolate_result.bed"/> </test> - + <test> + <param name="genomic_interval" value="interval_interpolate.bed"/> + <param name="genomic_feature" value="value_interpolate.bed"/> + <param name="allow_zeros" value="True" /> + <output name="out_file1" file="interpolate_result_zeros.bed"/> + </test> </tests> <help>