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annotate lastz_macros.xml @ 2:8e9252994649 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
author iuc
date Fri, 02 Mar 2018 12:06:35 -0500
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children c3767eaae954
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2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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1 <macros>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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2 <token name="@LASTZ_CONDA_VERSION@">1.0.4</token>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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3 <token name="@TARGET_INPUT_COMMAND_LINE@">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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4 #if $source.ref_source=="history":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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5 '${source.target}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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6 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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7 '${source.target_2bit.fields.path}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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8 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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9 </token>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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10 <xml name="target_input">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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11 <conditional name="source">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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12 <param name="ref_source" type="select" label="Select TARGET sequnce(s) to align against" help="If your TARGET is in history, choose 'from your history' option">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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13 <option value="cached">locally cached</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
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14 <option value="history">from your history</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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15 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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16 <when value="cached">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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17 <param name="target_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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18 <options from_data_table="lastz_seqs" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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19 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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20 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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21 <when value="history">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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22 <param name="target" type="data" format="fasta" label="Select a reference dataset" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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23 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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24 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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25 </xml>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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26 <xml name="citations">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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27 <citations>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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28 <citation type="bibtex">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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29 @misc{
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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30 githublastz,
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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31 author = {Harris, Robert},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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32 year = {2007},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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33 title = {Improved pairwise alignment of genomic DNA},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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34 publisher = {The Pennsylvania State University},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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35 journal = {Ph. D. Thesis},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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36 url = {http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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37 }
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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38 </citation>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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39 </citations>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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40 </xml>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
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41 </macros>