annotate lastz_macros.xml @ 11:37b497aa133f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c
author iuc
date Sun, 02 Jul 2023 12:10:46 +0000
parents 3e1ea2facca6
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bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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1 <macros>
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37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c
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2 <token name="@TOOL_VERSION@">1.04.22</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@TARGET_INPUT_COMMAND_LINE@"><![CDATA[
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5 #if $source.ref_source=="history":
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6 #if $source.target.is_of_type('fasta.gz'):
10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
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7 <(gunzip -c '${source.target}')
10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
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8 #else:
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9 '${source.target}'
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10 #end if
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11 #else:
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12 '${source.target_2bit.fields.path}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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13 #end if
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14 ]]>
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15 </token>
10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
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16 <token name="@query_input@"><![CDATA[
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17 #if $query.is_of_type('fasta.gz','fastq.gz'):
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18 <(gunzip -c '${query}')
10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
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19 #elif $query.is_of_type('fastq.bz2'):
10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
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20 <(bunzip2 -c '${query}')
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21 #else:
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22 '${query}'
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23 #end if
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24 ]]>
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25 </token>
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26 <xml name="bio_tools">
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27 <xrefs>
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28 <xref type="bio.tools">lastz</xref>
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29 </xrefs>
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30 </xml>
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31 <xml name="target_input">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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32 <conditional name="source">
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37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c
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33 <param name="ref_source" type="select" label="Select TARGET sequence(s) to align against" help="If your TARGET is in history, choose 'from your history' option">
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34 <option value="cached">locally cached</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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35 <option value="history">from your history</option>
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36 </param>
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37 <when value="cached">
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38 <param name="target_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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39 <options from_data_table="lastz_seqs" />
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40 </param>
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41 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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42 <when value="history">
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43 <param name="target" type="data" format="fasta,fasta.gz" label="Select a reference dataset" />
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44 </when>
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45 </conditional>
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46 </xml>
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47 <xml name="citations">
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48 <citations>
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49 <citation type="bibtex">
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50 @misc{
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51 githublastz,
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52 author = {Harris, Robert},
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53 year = {2007},
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54 title = {Improved pairwise alignment of genomic DNA},
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55 publisher = {The Pennsylvania State University},
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56 journal = {Ph. D. Thesis},
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57 url = {http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf},
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58 }
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59 </citation>
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60 </citations>
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61 </xml>
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62 </macros>