Mercurial > repos > devteam > weightedaverage
comparison 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 |
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1:90611e86a998 | 2:efa2b391e887 |
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1 <tool id="wtavg" name="Assign weighted-average" version="1.0.0"> | 1 <tool id="wtavg" name="Assign weighted-average" version="1.0.1"> |
2 <description> of the values of features overlapping an interval </description> | 2 <description> of the values of features overlapping an interval </description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.0.0">galaxy-ops</requirement> | 4 <requirement type="package" version="1.0.0">galaxy-ops</requirement> |
5 <requirement type="package" version="0.7.1">bx-python</requirement> | 5 <requirement type="package" version="0.7.1">bx-python</requirement> |
6 </requirements> | 6 </requirements> |
7 <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> | 7 <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> |
8 | 8 |
9 <inputs> | 9 <inputs> |
10 <param format="interval" name="genomic_interval" type="data" label="Genomic intervals (first dataset)" help="Dataset missing? See Note below."/> | 10 <param format="interval" name="genomic_interval" type="data" label="Genomic intervals (first dataset)" help="Dataset missing? See Note below."/> |
11 <param format="interval" name="genomic_feature" label="Genomic features (second dataset)" type="data" help="Make sure the value column is specified. See Note below." /> | 11 <param format="interval" name="genomic_feature" label="Genomic features (second dataset)" type="data" help="Make sure the value column is specified. See Note below." /> |
12 <param name="allow_zeros" label="Include zeros in calculations" type="boolean" help="Otherwise, skip them as bad values" truevalue="--allow_zeros" falsevalue="" checked="True" /> | |
12 </inputs> | 13 </inputs> |
13 <outputs> | 14 <outputs> |
14 <data format="input" name="out_file1" metadata_source="genomic_interval" /> | 15 <data format="input" name="out_file1" metadata_source="genomic_interval" /> |
15 </outputs> | 16 </outputs> |
16 <tests> | 17 <tests> |
17 <!-- Test data with valid values --> | 18 <!-- Test data with valid values --> |
18 <test> | 19 <test> |
19 <param name="genomic_interval" value="interval_interpolate.bed"/> | 20 <param name="genomic_interval" value="interval_interpolate.bed"/> |
20 <param name="genomic_feature" value="value_interpolate.bed"/> | 21 <param name="genomic_feature" value="value_interpolate.bed"/> |
22 <param name="allow_zeros" value="False" /> | |
21 <output name="out_file1" file="interpolate_result.bed"/> | 23 <output name="out_file1" file="interpolate_result.bed"/> |
22 </test> | 24 </test> |
23 | 25 <test> |
26 <param name="genomic_interval" value="interval_interpolate.bed"/> | |
27 <param name="genomic_feature" value="value_interpolate.bed"/> | |
28 <param name="allow_zeros" value="True" /> | |
29 <output name="out_file1" file="interpolate_result_zeros.bed"/> | |
30 </test> | |
24 </tests> | 31 </tests> |
25 <help> | 32 <help> |
26 | 33 |
27 | 34 |
28 .. class:: infomark | 35 .. class:: infomark |