Mercurial > repos > dave > genebed_maf_to_fasta

annotate macros.xml @ 0:be26293ade92 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
author dave
date Fri, 24 Jul 2020 12:35:57 -0400
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be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
dave
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1 <macros>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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2 <xml name="requirements">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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3 <requirement type="package" version="0.8.9">bx-python</requirement>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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4 <yield />
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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5 </xml>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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6 <xml name="citations">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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7 <citations>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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8 <citation type="doi">10.1093/bioinformatics/btr398</citation>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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9 </citations>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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10 </xml>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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11 <xml name="maf_source">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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12 <conditional name="maf_source_type">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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13 <param name="maf_source" type="select" label="MAF Source">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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14 <option value="cached" selected="true">Locally Cached Alignments</option>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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15 <option value="user">Alignments in Your History</option>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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16 </param>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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17 <when value="user">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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18 <param format="maf" name="mafFile" label="Choose alignments" type="data">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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19 <options>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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20 <filter type="data_meta" ref="input1" key="dbkey" />
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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21 </options>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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22 <validator type="dataset_ok_validator" />
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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23 </param>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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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">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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25 <options>
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26 <filter type="data_meta" ref="mafFile" key="species" />
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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27 </options>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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28 </param>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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29 </when>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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30 <when value="cached">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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31 <param name="mafType" type="select" label="Choose alignments">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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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"/>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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35 <column name="indexed_for" index="2"/>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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36 <column name="exists_in_maf" index="3" />
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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37 <column name="path" index="4" />
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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38 <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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39 <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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40 </options>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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41 </param>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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42 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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43 <options from_data_table="maf_indexes">
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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44 <column name="value" index="3"/>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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45 <filter type="multiple_splitter" column="3" separator=","/>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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46 </options>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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47 </param>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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48 </when>
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49 </conditional>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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50 </xml>
be26293ade92 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 8d55cabcec17915d959f672ecacfa851df1f4ca4-dirty"
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51 </macros>