Mercurial > repos > devteam > lastz
annotate lastz_macros.xml @ 7:10aca14c2332 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
author | iuc |
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date | Thu, 17 May 2018 04:29:13 -0400 |
parents | b6d7308c3728 |
children | 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> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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2 <token name="@LASTZ_CONDA_VERSION@">1.0.4</token> |
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10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
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3 <token name="@TARGET_INPUT_COMMAND_LINE@"><![CDATA[ |
5
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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4 #if $source.ref_source=="history": |
7
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
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5 #if $source.target.is_of_type('fasta.gz'): |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
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6 <(gunzip -c '${source.target}') |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
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7 #else: |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
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8 '${source.target}' |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
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diff
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9 #end if |
5
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
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10 #else: |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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11 '${source.target_2bit.fields.path}' |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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12 #end if |
7
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
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13 ]]> |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
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14 </token> |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
changeset
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15 <token name="@query_input@"><![CDATA[ |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
changeset
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16 #if $query.is_of_type('fasta.gz','fastq.gz'): |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
changeset
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17 <(gunzip -c '${query}') |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
changeset
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18 #elif $query.is_of_type('fastq.bz2'): |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
changeset
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19 <(bunzip2 -c '${query}') |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
changeset
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20 #else: |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
changeset
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21 '${query}' |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
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22 #end if |
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
changeset
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23 ]]> |
5
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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changeset
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24 </token> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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changeset
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25 <xml name="target_input"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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changeset
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26 <conditional name="source"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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27 <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"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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28 <option value="cached">locally cached</option> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
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29 <option value="history">from your history</option> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
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30 </param> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
diff
changeset
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31 <when value="cached"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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32 <param name="target_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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33 <options from_data_table="lastz_seqs" /> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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34 </param> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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35 </when> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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changeset
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36 <when value="history"> |
7
10aca14c2332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents:
6
diff
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37 <param name="target" type="data" format="fasta,fasta.gz" label="Select a reference dataset" /> |
5
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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38 </when> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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39 </conditional> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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40 </xml> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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41 <xml name="citations"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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42 <citations> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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43 <citation type="bibtex"> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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44 @misc{ |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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45 githublastz, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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46 author = {Harris, Robert}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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47 year = {2007}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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48 title = {Improved pairwise alignment of genomic DNA}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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49 publisher = {The Pennsylvania State University}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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50 journal = {Ph. D. Thesis}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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51 url = {http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf}, |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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52 } |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
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53 </citation> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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54 </citations> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
parents:
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55 </xml> |
bd84ff27bc16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56
devteam
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56 </macros> |