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comparison WeightedAverage.xml @ 2:efa2b391e887 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
author devteam
date Wed, 05 Oct 2016 13:39:38 -0400
parents 90611e86a998
children
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1:90611e86a998 2:efa2b391e887
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