Mercurial > repos > iuc > coverm_contig
annotate macros.xml @ 0:6941d0d453ba draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
author | iuc |
---|---|
date | Tue, 26 Apr 2022 15:27:37 +0000 |
parents | |
children | 688a777e1b19 |
rev | line source |
---|---|
0
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
1 <macros> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
2 <xml name="requirements"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
3 <requirements> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
4 <requirement type="package">coverm</requirement> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
5 </requirements> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
6 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
7 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
8 <token name="@TOOL_VERSION@">0.2.1</token> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
9 <token name="@VERSION_SUFFIX@">0</token> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
10 <xml name="citation"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
11 <citations> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
12 <citation type="bibtex"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
13 @misc{githubCoverm, |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
14 author = {B J. Woodcroft}, |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
15 year = {2021}, |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
16 title = {CoverM}, |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
17 publisher = {GitHub}, |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
18 journal = {GitHub repository}, |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
19 url = {https://github.com/wwood/CoverM} |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
20 } |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
21 </citation> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
22 </citations> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
23 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
24 <xml name="genome_opt"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
25 <conditional name="genome"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
26 <param name="ref_or_genome" type="select" label="Select if you want to specify additional genome files."> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
27 <option value="genomic">yes</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
28 <option value="none" selected="true">No (Only when BAM files are provided)</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
29 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
30 <when value="none"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
31 <param argument="--single-genome" type="boolean" truevalue="--single-genome" falsevalue="" checked="false" label="All contigs are from the same genome."/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
32 <param type="text" name="separator" optional="true" label="Character, that separates genome names from contig names in the reference file." > |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
33 <sanitizer> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
34 <valid initial="string.punctuation"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
35 </valid> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
36 </sanitizer> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
37 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
38 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
39 <when value="genomic"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
40 <conditional name="genomic"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
41 <param type="select" label="Reference genome source" name="source"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
42 <option value="history" selected="true">History</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
43 <option value="builtin">Built-in</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
44 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
45 <when value="history"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
46 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
47 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
48 <when value="builtin"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
49 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
50 <options from_data_table="all_fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
51 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
52 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
53 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
54 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
55 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
56 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
57 <xml name="genome"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
58 <conditional name="genome"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
59 <param name="ref_or_genome" type="select" label="Reference sequence mode" help="Select if you want to specify genome file(s) or a FASTA reference file or both. NOTE: If genomic FASTA files are specified, then reference is not needed as a reference FASTA file can be derived by concatenating input genomes. However, while not necessary, reference can be specified if an alternate reference sequence set is desired."> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
60 <option value="genomic" selected="true">Reference genome</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
61 <option value="reference">Contigs (e.g. concatenated genomes or metagenome assembly)</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
62 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
63 <when value="genomic"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
64 <conditional name="genomic"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
65 <param type="select" label="Reference genome source" name="source"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
66 <option value="history" selected="true">History</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
67 <option value="builtin">Built-in</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
68 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
69 <when value="history"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
70 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
71 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
72 <when value="builtin"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
73 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
74 <options from_data_table="all_fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
75 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
76 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
77 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
78 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
79 <when value="reference"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
80 <param type="data" name="ref_source" multiple="true" label="Contigs file(s)" format="fasta" help="If multiple references FASTA files are provided and 'sharded' is specified, then reads will be mapped to references separately as sharded BAMs."/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
81 <conditional name="cond_single_genome"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
82 <param name="single_genome" type="select" label="All contigs are from a single genome"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
83 <option value="--single-genome">True</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
84 <option value="false">False</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
85 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
86 <when value="--single-genome"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
87 <param type="data" name="genome_definition" format="tsv" optional="true" label="File containing newline-separated list of genome_name and contig, separated by tab, to define the genome of each contig." /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
88 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
89 <when value="false"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
90 <param type="text" argument="--separator" optional="true" label="Character, that separates genome names from contig names in the reference file." > |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
91 <sanitizer> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
92 <valid initial="string.punctuation"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
93 </valid> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
94 </sanitizer> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
95 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
96 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
97 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
98 <conditional name="add_genome"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
99 <param name="add_genome" type="boolean" label="Add additional Genome Files"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
100 <when value="true"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
101 <conditional name="add_genomic"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
102 <param type="select" label="Reference genome source" name="source"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
103 <option value="history" selected="true">History</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
104 <option value="builtin">Built-in</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
105 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
106 <when value="history"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
107 <param type="data" name="fasta_history" multiple="true" label="Single FASTA file of contigs" format="fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
108 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
109 <when value="builtin"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
110 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
111 <options from_data_table="all_fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
112 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
113 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
114 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
115 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
116 <when value="false"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
117 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
118 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
119 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
120 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
121 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
122 <xml name="reads_for_contig"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
123 <conditional name="reads"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
124 <param type="select" label="Read type" name="read_type"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
125 <option value="paired">Paired end</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
126 <option value="paired_collection" selected="true">Paired collection</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
127 <option value="single">Single ended</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
128 <option value="interleaved">Interleaved</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
129 <option value="bam">BAM file(s)</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
130 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
131 <when value="paired"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
132 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
133 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
134 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
135 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
136 <when value="paired_collection"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
137 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
138 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
139 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
140 <when value="single"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
141 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
142 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
143 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
144 <when value="interleaved"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
145 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
146 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
147 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
148 <when value="bam"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
149 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
150 <param type="data" name="ref_fasta_history" optional="true" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
151 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
152 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
153 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
154 <xml name="reads"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
155 <conditional name="reads"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
156 <param type="select" label="Read type" name="read_type"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
157 <option value="single">Single ended</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
158 <option value="paired">Paired end</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
159 <option value="paired_collection" selected="true">Paired collection</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
160 <option value="interleaved">Interleaved</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
161 <option value="bam">BAM file(s)</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
162 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
163 <when value="paired"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
164 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
165 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
166 <expand macro="genome"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
167 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
168 <when value="paired_collection"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
169 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="Collection of paired-reads" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
170 <expand macro="genome"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
171 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
172 <when value="single"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
173 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
174 <expand macro="genome"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
175 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
176 <when value="interleaved"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
177 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
178 <expand macro="genome"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
179 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
180 <when value="bam"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
181 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
182 <expand macro="genome_opt"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
183 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
184 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
185 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
186 <xml name="add_reads"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
187 <section name="add_reads" title="Add an additional read"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
188 <conditional name="extra_read"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
189 <param type="select" label="Read type" optional="true" name="read_type"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
190 <option value="none" selected="true">None</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
191 <option value="paired">Paired end</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
192 <option value="paired_collection">Paired collection</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
193 <option value="single">Single ended</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
194 <option value="interleaved">Interleaved</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
195 <option value="bam">BAM file(s)</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
196 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
197 <when value="none"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
198 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
199 <when value="paired"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
200 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
201 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
202 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
203 <when value="paired_collection"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
204 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
205 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
206 <when value="single"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
207 <param type="data" format="@INPUT_FORMATS@" name="single" multiple="true" label="Single read" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
208 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
209 <when value="interleaved"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
210 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
211 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
212 <when value="bam"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
213 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
214 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
215 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
216 </section> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
217 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
218 <xml name="mapping"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
219 <section name="mapping" title="Mapping options" expanded="false"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
220 <param argument="--mapper" optional="true" type="select" label="Mapper" help="Underlying mapping software used. Default: minimap2-sr" > |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
221 <option value="minimap2-sr">minimap2 with '-x sr' option</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
222 <option value="minimap2-ont">minimap2 with '-x map-ont' option</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
223 <option value="minimap2-pb">minimap2 with '-x map-pb' option</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
224 <option value="minimap2-no-preset">minimap2 with no '-x' option</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
225 <option value="bwa-mem">BWA-MEM using default parameters</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
226 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
227 <param argument="--min_read-aligned-length" type="integer" min="0" value="0" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
228 label="Min read aligned length" help="Exclude reads with smaller numbers of aligned bases. Default: 0" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
229 <param argument="--min_read-percent-identity" type="float" min="0" max="100" value="0" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
230 label="Min read percent identity" help="Exclude reads by overall percent identity e.g. 95 for 95%. Default: 0" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
231 <param argument="--min_read-aligned-percent" type="float" min="0" max="100" value="0" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
232 label="Min read aligned percentage" help="Exclude reads by percent aligned bases e.g. 95 means 95% |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
233 of the read's bases must be aligned. Default: 0" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
234 <param argument="--min_read-aligned-length-pair" type="integer" min="0" value="0" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
235 label="Min read aligned length pair" help="Exclude pairs with smaller numbers of aligned bases. |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
236 Implies --proper-pairs-only. Default: 0" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
237 <param argument="--min_read-percent-identity-pair" type="float" min="0" max="100" value="0" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
238 label="Min read percent identity pair" help="Exclude pairs by overall percent identity e.g. 95 for 95%. |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
239 Implies --proper-pairs-only. Default: 0" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
240 <param argument="--min_read-aligned-percent-pair" type="float" min="0" max="100" value="0" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
241 label="Min read aligned percentage pair" help="Exclude reads by percent aligned bases e.g. 95 means 95% of |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
242 the read's bases must be aligned. Implies --proper-pairs-only. Default: 0" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
243 <param argument="--proper-pairs-only" type="boolean" truevalue="--proper-pairs-only" falsevalue="" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
244 label="Require reads to be mapped as proper pairs" help="Default: not set"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
245 <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue="" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
246 label="Exclude supplementary alignments" help="Default: not set"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
247 </section> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
248 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
249 <xml name="coverage"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
250 <section name="cov" title="Coverage calculation options" expanded="false"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
251 <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
252 <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
253 <conditional name="cond_methods"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
254 <param name="trimmed_mean" type="boolean" falsevalue="" truevalue="trimmed_mean" label="Trimmed mean"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
255 <when value="trimmed_mean"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
256 <param name="trim_min" type="integer" min="0" value="5" label="Trim min" help="Remove this smallest fraction of positions when calculating trimmed_mean default: 5"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
257 <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
258 </when> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
259 <when value=""/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
260 </conditional> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
261 <param name="covered_bases" type="boolean" falsevalue="" truevalue="covered_bases" label="Covered bases"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
262 <param name="covered_fraction" type="boolean" falsevalue="" truevalue="covered_fraction" label="Covered fraction"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
263 <param name="variance" type="boolean" falsevalue="" truevalue="variance" label="Variance"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
264 <param name="length" type="boolean" falsevalue="" truevalue="length" label="Length"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
265 <param name="count" type="boolean" falsevalue="" truevalue="count" label="Count"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
266 <param name="metabat" type="boolean" falsevalue="" truevalue="metabat" label="MetaBAT"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
267 <param name="coverage_histogram" type="boolean" falsevalue="" truevalue="coverage_histogram" label="Coverage histogram"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
268 <param name="reads_per_base" type="boolean" falsevalue="" truevalue="reads_per_base" label="Reads per base"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
269 <param name="rpkm" type="boolean" falsevalue="" truevalue="rpkm" label="RPKM"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
270 <param name="tpm" type="boolean" falsevalue="" truevalue="tpm" label="TPKM"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
271 <param name="min_covered_fraction" type="integer" min="0" optional="true" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
272 label="Min covered fraction" help="Genomes with less coverage than this reported as having zero coverage. Default: 10"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
273 <param name="contig_end_exclusion" type="integer" min="0" optional="true" |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
274 label="Contig end exclusion" help="Exclude bases at the ends of reference sequences from calculation. Default: 75"/> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
275 </section> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
276 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
277 <xml name="out"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
278 <section name="out" title="Output options" expanded="false"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
279 <param name="output_format" type="select" label="Shape of output" help="'Sparse' for long format, 'dense' for species-by-site. Default: dense]"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
280 <option value="dense" selected="true">Dense</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
281 <option value="sparse">Sparse</option> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
282 </param> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
283 <param name="no_zeros" type="boolean" truevalue="--no-zeros" falsevalue="" optional="true" label="Omit printing of genomes that have zero coverage" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
284 <param argument="--dereplication-output-cluster-definition" type="boolean" truevalue="--dereplication-output-cluster-definition" falsevalue="" label="Output a file of representative TAB member lines." /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
285 <param argument="--dereplication-output-representative-fasta-directory-copy" type="boolean" truevalue="--dereplication-output-representative-fasta-directory-copy" falsevalue="" label="Output representative genomes" /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
286 </section> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
287 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
288 <xml name="citations"> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
289 <citations> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
290 <yield /> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
291 </citations> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
292 </xml> |
6941d0d453ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff
changeset
|
293 </macros> |