Mercurial > repos > devteam > lastz

annotate lastz_macros.xml @ 10:37ba0585e60b draft default tip

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/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
author iuc
date Thu, 05 Feb 2026 12:51:47 +0000
parents da6f44d06921
children
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>
10
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
2 <token name="@TOOL_VERSION@">1.04.52</token>
7
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>
10
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
4 <token name="@PROFILE@">25.0</token>
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
5 <xml name="requirements">
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
6 <requirements>
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">lastz</requirement>
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
8 <requirement type="package" version="1.14">samtools</requirement>
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
9 <requirement type="package" version="3.6.3">r-base</requirement>
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
10 <requirement type="package" version="1.0.8">bzip2</requirement>
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
11 </requirements>
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
12 </xml>
37ba0585e60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94
iuc
parents: 8
diff changeset
13
3
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
14 <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
15 #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
16 #if $source.target.is_of_type('fasta.gz'):
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
17 <(gunzip -c '${source.target}')
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
18 #else:
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
19 '${source.target}'
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
20 #end if
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
21 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
22 '${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
23 #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
24 ]]>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
25 </token>
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
26 <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
27 #if $query.is_of_type('fasta.gz','fastq.gz'):
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
28 <(gunzip -c '${query}')
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
29 #elif $query.is_of_type('fastq.bz2'):
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
30 <(bunzip2 -c '${query}')
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
31 #else:
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
32 '${query}'
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
33 #end if
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
iuc
parents: 2
diff changeset
34 ]]>
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
35 </token>
6
ac0ffffa649e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
36 <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
37 <xrefs>
ac0ffffa649e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
38 <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
39 </xrefs>
ac0ffffa649e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
40 </xml>
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
41 <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
42 <conditional name="source">
8
da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c
iuc
parents: 7
diff changeset
43 <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">
2
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
44 <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
45 <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
46 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
47 <when value="cached">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
48 <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
49 <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
50 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
51 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
52 <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
53 <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
54 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
55 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
56 </xml>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
57 <xml name="citations">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
58 <citations>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
59 <citation type="bibtex">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
60 @misc{
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
61 githublastz,
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
62 author = {Harris, Robert},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
63 year = {2007},
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
64 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
65 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
66 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
67 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
68 }
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
69 </citation>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
70 </citations>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
71 </xml>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa
iuc
parents:
diff changeset
72 </macros>