Mercurial > repos > iuc > cutesv
comparison macros.xml @ 0:c0f8fe52948e draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
author | iuc |
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date | Thu, 24 Sep 2020 15:11:57 +0000 |
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-1:000000000000 | 0:c0f8fe52948e |
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1 <macros> | |
2 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> | |
3 <token name="@TOOL_VERSION@">1.0.8</token> | |
4 <xml name="reference_interface"> | |
5 <conditional name="reference_source"> | |
6 <param name="ref_selector" type="select" label="Choose the source for the reference genome"> | |
7 <option value="cached">Locally cached</option> | |
8 <option value="history">History</option> | |
9 </param> | |
10 <when value="cached"> | |
11 <param argument="--ref" type="select" label="Reference genome"> | |
12 <options from_data_table="fasta_indexes"> | |
13 <!-- <filter type="data_meta" column="dbkey" key="dbkey" ref="input_sample_file" /> --> | |
14 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> | |
15 </options> | |
16 </param> | |
17 </when> | |
18 <when value="history"> | |
19 <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" /> | |
20 </when> | |
21 </conditional> | |
22 </xml> | |
23 <xml name="adv_shared_1"> | |
24 <param name="batches" type="integer" value="10000000" min="0" label="Batches" help="Batch of genome segmentation interval." /> | |
25 <param name="max_split_parts" type="integer" value="7" min="0" label="Maximum number of split segments" help="Maximum number of split segments a read may be aligned before it is ignored." /> | |
26 <param name="min_mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Minimum mapping quality value of alignment to be taken into account." /> | |
27 <param name="min_read_len" type="integer" value="500" min="0" label="Minimum read length" help="Ignores reads that only report alignments with not longer than bp." /> | |
28 <param name="merge_del_threshold" type="integer" value="0" min="0" label="Maximum distance of deletions" help="Maximum distance of deletion signals to be merged." /> | |
29 <param name="merge_ins_threshold" type="integer" value="100" min="0" label="Maximum distance of insertions" help="Maximum distance of insertion signals to be merged." /> | |
30 <param name="min_support" type="integer" value="10" min="0" label="Minimum number of reads that support a SV" help="Minimum number of reads that support a SV to be reported." /> | |
31 <param name="min_size" type="integer" value="30" min="0" label="Minimum SV length" help="Minimum length of SV to be reported. " /> | |
32 <param name="max_size" type="integer" value="100000" min="0" label="Maximum SV length" help="Maximum length of SV to be reported." /> | |
33 <section name="genotyping" title="Genotyping settings" expanded="false"> | |
34 <param name="genotype" type="boolean" checked="False" label="Genotype" help="Enable to generate genotypes." /> | |
35 <param name="gt_round" type="integer" value="500" min="1" label="Maximum iterations for genotyping" help="Maximum round of iteration for alignments searching if perform genotyping." /> | |
36 </section> | |
37 </xml> | |
38 <xml name="adv_pb_clr"> | |
39 <section name="seq_method" title="PacBio CLR settings" expanded="false"> | |
40 <param name="max_cluster_bias_INS" type="integer" value="100" min="0" label="Maximum cluster distance (insertion)" help="Maximum distance to cluster read together for insertion." /> | |
41 <param name="diff_ratio_merging_INS" type="float" value="0.3" min="0" max="1" label="Breakpoints merge threshold (insertion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for insertion." /> | |
42 <param name="max_cluster_bias_DEL" type="integer" value="200" min="0" label="Maximum cluster distance (deletion)" help="Maximum distance to cluster read together for deletion." /> | |
43 <param name="diff_ratio_merging_DEL" type="float" value="0.5" min="0" max="1" label="Breakpoints merge threshold (deletion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for deletion." /> | |
44 </section> | |
45 </xml> | |
46 <xml name="adv_pb_ccs"> | |
47 <section name="seq_method" title="PacBio CCS(HIFI) settings" expanded="false"> | |
48 <param name="max_cluster_bias_INS" type="integer" value="1000" min="0" label="Maximum cluster distance (insertion)" help="Maximum distance to cluster read together for insertion." /> | |
49 <param name="diff_ratio_merging_INS" type="float" value="0.9" min="0" max="1" label="Breakpoints merge threshold (insertion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for insertion." /> | |
50 <param name="max_cluster_bias_DEL" type="integer" value="1000" min="0" label="Maximum cluster distance (deletion)" help="Maximum distance to cluster read together for deletion." /> | |
51 <param name="diff_ratio_merging_DEL" type="float" value="0.5" min="0" max="1" label="Breakpoints merge threshold (deletion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for deletion." /> | |
52 </section> | |
53 </xml> | |
54 <xml name="adv_ont"> | |
55 <section name="seq_method" title="ONT settings" expanded="false"> | |
56 <param name="max_cluster_bias_INS" type="integer" value="100" min="0" label="Maximum cluster distance (insertion)" help="Maximum distance to cluster read together for insertion." /> | |
57 <param name="diff_ratio_merging_INS" type="float" value="0.3" min="0" max="1" label="Breakpoints merge threshold (insertion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for insertion." /> | |
58 <param name="max_cluster_bias_DEL" type="integer" value="100" min="0" label="Maximum cluster distance (deletion)" help="Maximum distance to cluster read together for deletion." /> | |
59 <param name="diff_ratio_merging_DEL" type="float" value="0.3" min="0" max="1" label="Breakpoints merge threshold (deletion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for deletion." /> | |
60 </section> | |
61 </xml> | |
62 <xml name="adv_other"> | |
63 <section name="seq_method" title="Advanced method settings" expanded="true"> | |
64 <param name="max_cluster_bias_INS" type="integer" value="100" min="0" label="Maximum cluster distance (insertion)" help="Maximum distance to cluster read together for insertion." /> | |
65 <param name="diff_ratio_merging_INS" type="float" value="0.3" min="0" max="1" label="Breakpoints merge threshold (insertion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for insertion." /> | |
66 <param name="max_cluster_bias_DEL" type="integer" value="200" min="0" label="Maximum cluster distance (deletion)" help="Maximum distance to cluster read together for deletion." /> | |
67 <param name="diff_ratio_merging_DEL" type="float" value="0.5" min="0" max="1" label="Breakpoints merge threshold (deletion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for deletion." /> | |
68 </section> | |
69 </xml> | |
70 <xml name="adv_shared_2"> | |
71 <param name="max_cluster_bias_INV" type="integer" value="500" min="0" label="Maximum distance to cluster (inversion)" help="Maximum distance to cluster read together for inversion." /> | |
72 <param name="max_cluster_bias_DUP" type="integer" value="500" min="0" label="Maximum distance to cluster (duplication)" help="Maximum distance to cluster read together for duplication." /> | |
73 <param name="max_cluster_bias_TRA" type="integer" value="50" min="0" label="Maximum distance to cluster (translocation)" help="Maximum distance to cluster read together for translocation." /> | |
74 <param name="diff_ratio_filtering_TRA" type="float" value="0.6" min="0" max="1" label="Breakpoints filter threshold (translocation)" help="Filter breakpoints with basepair identity less than the ratio of default for translocation." /> | |
75 <param name="report_readid" type="boolean" checked="False" label="Report read id" help="Enable to report supporting read ids for each SV." /> | |
76 </xml> | |
77 </macros> |