Mercurial > repos > iuc > genebed_maf_to_fasta

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 5745d4b9f7fe594eeb92967313e5bd9e8f24a6f1"
author iuc
date Thu, 25 Nov 2021 14:20:59 +0000
parents 020c78e91cc5
children
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f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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1 <macros>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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2 <xml name="requirements">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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3 <requirement type="package" version="0.8.9">bx-python</requirement>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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4 <yield />
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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5 </xml>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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6 <xml name="citations">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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7 <citations>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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8 <citation type="doi">10.1093/bioinformatics/btr398</citation>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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9 </citations>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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10 </xml>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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11 <xml name="maf_source">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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12 <conditional name="maf_source_type">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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13 <param name="maf_source" type="select" label="MAF Source">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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14 <option value="cached" selected="true">Locally Cached Alignments</option>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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15 <option value="user">Alignments in Your History</option>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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16 </param>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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17 <when value="user">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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18 <param format="maf" name="maf_file" label="Choose alignments" type="data">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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19 <options>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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20 <filter type="data_meta" ref="input1" key="dbkey" />
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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21 </options>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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22 <validator type="dataset_ok_validator" />
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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23 </param>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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24 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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25 <options>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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26 <filter type="data_meta" ref="maf_file" key="species" />
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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27 </options>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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28 </param>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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29 </when>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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30 <when value="cached">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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31 <param name="mafType" type="select" label="Choose alignments">
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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32 <options from_data_table="maf_indexes">
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33 <column name="name" index="0"/>
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34 <column name="value" index="1"/>
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35 <column name="indexed_for" index="2"/>
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36 <column name="exists_in_maf" index="3" />
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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37 <column name="path" index="4" />
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38 </options>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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39 </param>
1
020c78e91cc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 95632be9aca24769ac192f2eb6a0454af21eff9e"
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40 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment. Results may not be easily predictable if the input species does not exist in the cached multi-alignment">
0
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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41 <options from_data_table="maf_indexes">
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42 <column name="value" index="3"/>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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43 <filter type="multiple_splitter" column="3" separator=","/>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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44 </options>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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45 </param>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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46 </when>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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47 </conditional>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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48 </xml>
f24a9ff28d3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
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49 </macros>