Mercurial > repos > miller-lab > genome_diversity

annotate diversity_pi.xml @ 27:8997f2ca8c7a

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Update to Miller Lab devshed revision bae0d3306d3b
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 15 Jul 2013 10:47:35 -0400
parents 248b06e86022
children a631c2f6d913
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248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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1 <tool id="gd_diversity_pi" name="Diversity" version="1.0.0">
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2 <description>&amp;pi;</description>
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3
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4 <command interpreter="python">
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5 #import json
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6 #import base64
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7 #import zlib
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8 #set $ind_names = $input.dataset.metadata.individual_names
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9 #set $ind_colms = $input.dataset.metadata.individual_columns
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10 #set $ind_dict = dict(zip($ind_names, $ind_colms))
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11 #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
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12 #set $ind_comp = zlib.compress($ind_json, 9)
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13 #set $ind_arg = base64.b64encode($ind_comp)
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14 diversity_pi.py '$input' '$coverage_input' '$indiv_input' '$min_coverage' '$output' '$ind_arg'
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15 </command>
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16
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17 <inputs>
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18 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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19 <param name="coverage_input" type="data" format="interval" label="Coverage dataset" />
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20 <param name="indiv_input" type="data" format="gd_indivs" label="Population Individuals" />
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21 <param name="min_coverage" type="integer" min="1" value="1" label="Minimum coverage" />
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22 </inputs>
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23
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24 <outputs>
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25 <data name="output" format="txt" metadata_source="input" />
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26 </outputs>
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27
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28 <help>
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29 </help>
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30 </tool>