Mercurial > repos > devteam > lastz

annotate lastz_macros.xml @ 7:86f2c3695694 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2"
author iuc
date Sat, 27 Nov 2021 10:40:44 +0000
parents ac0ffffa649e
children da6f44d06921
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
1 <macros>
7
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2"
iuc
parents: 6
diff changeset
2 <token name="@TOOL_VERSION@">1.04.15</token>
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2"
iuc
parents: 6
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
3
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
4 <token name="@TARGET_INPUT_COMMAND_LINE@"><![CDATA[
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
5 #if $source.ref_source=="history":
3
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
6 #if $source.target.is_of_type('fasta.gz'):
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
7 <(gunzip -c '${source.target}')
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
8 #else:
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
9 '${source.target}'
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
10 #end if
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
11 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
12 '${source.target_2bit.fields.path}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
13 #end if
3
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
14 ]]>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
15 </token>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
16 <token name="@query_input@"><![CDATA[
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
17 #if $query.is_of_type('fasta.gz','fastq.gz'):
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
18 <(gunzip -c '${query}')
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
19 #elif $query.is_of_type('fastq.bz2'):
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
20 <(bunzip2 -c '${query}')
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
21 #else:
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
22 '${query}'
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
23 #end if
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
24 ]]>
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
25 </token>
6
ac0ffffa649e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
26 <xml name="bio_tools">
ac0ffffa649e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
27 <xrefs>
ac0ffffa649e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
28 <xref type="bio.tools">lastz</xref>
ac0ffffa649e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
29 </xrefs>
ac0ffffa649e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
30 </xml>
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
31 <xml name="target_input">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
32 <conditional name="source">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
33 <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
iuc
parents:
diff changeset
34 <option value="cached">locally cached</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
35 <option value="history">from your history</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
36 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
37 <when value="cached">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
38 <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
iuc
parents:
diff changeset
39 <options from_data_table="lastz_seqs" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
40 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
41 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
42 <when value="history">
3
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
43 <param name="target" type="data" format="fasta,fasta.gz" label="Select a reference dataset" />
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
44 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
45 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
46 </xml>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
47 <xml name="citations">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
48 <citations>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
49 <citation type="bibtex">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
50 @misc{
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
51 githublastz,
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
52 author = {Harris, Robert},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
53 year = {2007},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
54 title = {Improved pairwise alignment of genomic DNA},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
55 publisher = {The Pennsylvania State University},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
56 journal = {Ph. D. Thesis},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
57 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
iuc
parents:
diff changeset
58 }
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
59 </citation>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
60 </citations>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
61 </xml>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
62 </macros>