Mercurial > repos > thanhlv > galru
comparison galru.xml @ 0:685f2f21f160 draft
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author | thanhlv |
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date | Tue, 02 Jun 2020 10:07:09 -0400 |
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children | f435723251c3 |
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-1:000000000000 | 0:685f2f21f160 |
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1 <tool id="galru" name="galru" version="@VERSION@"> | |
2 <description>Long read spoligotyping for Mycobacterium tuberculosis</description> | |
3 <macros> | |
4 <token name="@VERSION@">1.0.0</token> | |
5 </macros> | |
6 <requirements> | |
7 <requirement type="package" version="@VERSION@">galru</requirement> | |
8 </requirements> | |
9 <version_command>galru --version</version_command> | |
10 <command detect_errors="exit_code"><![CDATA[ | |
11 galru | |
12 --technology $technology | |
13 #if str($cas_input.cas_select) == "history": | |
14 --cas_fasta '$cas_input.cas_file' | |
15 #end if | |
16 --gene_start_offset $gene_start_offset | |
17 --min_mapping_quality $min_mapping_quality | |
18 --qcov_margin $qcov_margin | |
19 --min_bitscore $min_bitscore | |
20 --min_identity $min_identity | |
21 --threads \${GALAXY_SLOTS:-4} | |
22 $extended | |
23 $debug | |
24 $verbose | |
25 --output_file $output | |
26 $fastq | |
27 ]]> </command> | |
28 | |
29 <inputs> | |
30 <param name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Uncorrected long reads"/> | |
31 <conditional name="cas_input"> | |
32 <param name="cas_select" type="select" label="CAS file"> | |
33 <option selected="true" value="bundle">Use bundled CAS file</option> | |
34 <option value="history">Use a fasta file in the history</option> | |
35 </param> | |
36 <when value="history"> | |
37 <param name="cas_file" type="data" format="fasta,fasta.gz" label="Select a CAS file"/> | |
38 </when> | |
39 </conditional> | |
40 <param name="technology" type="select" optional="false" label="Sequencing technology"> | |
41 <option value="map-ont">map-ont</option> | |
42 <option value="map-pb">map-pb</option> | |
43 <option value="ava-ont">ava-ont</option> | |
44 <option value="ava-pb">ava-pb</option> | |
45 </param> | |
46 <param name="extended" argument="--extended_results" type="boolean" truevalue="--extended_results" falsevalue="" checked="false" label="Output extended results" /> | |
47 <param name="gene_start_offset" argument="--gene_start_offset" type="integer" min="0" value="30" label="Only count CRISPR reads which cover this base"/> | |
48 <param name="min_mapping_quality" argument="--min_mapping_quality" type="integer" min="0" value="10" label="Minimum mapping quality score"/> | |
49 <param name="qcov_margin" argument="--qcov_margin" type="integer" min="0" value="100" label="Maximum perc coverage difference between CRISPR and read"/> | |
50 <param name="min_bitscore" argument="--min_bitscore" type="integer" min="0" value="38" label="Minimum blast bitscore"/> | |
51 <param name="min_identity" argument="--min_identity" type="integer" min="0" value="95" label="Minimum blast identity"/> | |
52 <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Turn on debugging" /> | |
53 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on verbose output" /> | |
54 </inputs> | |
55 <outputs> | |
56 <data name="output" format="tabular" label="${tool.name} on ${on_string} Output"/> | |
57 <data name="log" format="text" label="${tool.name} on ${on_string} Log"> | |
58 <filter>debug is True</filter> | |
59 </data> | |
60 </outputs> | |
61 | |
62 <help><![CDATA[ | |
63 | |
64 Documentation can be found at `<https://github.com/quadram-institute-bioscience/galru>`_. | |
65 | |
66 ]]> </help> | |
67 <citations> | |
68 <citation type="doi">10.1101/2020.05.31.126490v1</citation> | |
69 </citations> | |
70 </tool> |