Mercurial > repos > estrain > confindr
comparison confindr.xml @ 0:454e2f1ccff4 draft
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author | estrain |
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date | Sun, 21 Oct 2018 08:19:08 -0400 |
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-1:000000000000 | 0:454e2f1ccff4 |
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1 <tool id="confindr" name="confindr" label="Detect sequence contamination using rMLST" version="0.1.3"> | |
2 <requirements> | |
3 <requirement type="package" version="0.4.3">confindr</requirement> | |
4 </requirements> | |
5 <command detect_errors="exit_code"><![CDATA[ | |
6 mkdir in out; | |
7 #if $jobtype.select == "fastq_single" | |
8 perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name; | |
9 #else if $jobtype.select == "fastq_fr" | |
10 perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name; | |
11 perl $__tool_directory__/makein.pl in $jobtype.fastq2 $jobtype.fastq2.name; | |
12 #else if $jobtype.select == "fastq_pair" | |
13 perl $__tool_directory__/makein.pl in $jobtype.coll.forward $jobtype.coll.forward.name; | |
14 perl $__tool_directory__/makein.pl in $jobtype.coll.reverse $jobtype.coll.reverse.name; | |
15 #end if | |
16 confindr.py -i in -o out | |
17 #if $options.select=="advanced" | |
18 #if $options.threads | |
19 -t $options.threads | |
20 #end if | |
21 #if $options.quality | |
22 -q $options.quality | |
23 #end if | |
24 #if $options.basecut | |
25 -b $options.basecut | |
26 #end if | |
27 #if $options.basefrac | |
28 -bf $options.basefrac | |
29 #end if | |
30 #if $options.datatype | |
31 -dt $options.datatype | |
32 #end if | |
33 #else if $options.select=="basic" | |
34 -t \${GALAXY_SLOTS:-1} | |
35 #end if | |
36 ]]></command> | |
37 <inputs> | |
38 <conditional name="jobtype"> | |
39 <param name="select" type="select" label="Select Input"> | |
40 <option value="fastq_single">Single FASTQ</option> | |
41 <option value="fastq_fr">Forward and Reverse FASTQ</option> | |
42 <option value="fastq_pair">Paired FASTQ Collection</option> | |
43 </param> | |
44 <when value="fastq_single"> | |
45 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" /> | |
46 </when> | |
47 <when value="fastq_fr"> | |
48 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward FASTQ" /> | |
49 <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse FASTQ" /> | |
50 </when> | |
51 <when value="fastq_pair"> | |
52 <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> | |
53 </when> | |
54 </conditional> | |
55 <conditional name="options"> | |
56 <param name="select" type="select" label="Basic or Advanced Settings"> | |
57 <option value="basic">Basic</option> | |
58 <option value="advanced">Advanced</option> | |
59 </param> | |
60 <when value="advanced"> | |
61 <param name="threads" optional="true" type="integer" label="Number of threads (Default=all)" value=""/> | |
62 <param name="quality" optional="true" type="integer" label="Base quality needed to support a multiple allele call (Default=20)" value=""/> | |
63 <param name="basecut" optional="true" type="integer" label="Number of bases necessary to support a multiple allele call (Default=2)" value=""/> | |
64 <param name="basefrac" optional="true" type="float" label="Fraction of bases necessary to support a multiple call." value=""> | |
65 <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/> | |
66 </param> | |
67 <param name="datatype" type="select" label="Data Type"> | |
68 <option value="Illumina">Illumina</option> | |
69 <option value="Nanopore">Nanopore</option> | |
70 <option value="auto">auto</option> | |
71 </param> | |
72 </when> | |
73 <when value="basic"> | |
74 </when> | |
75 </conditional> | |
76 </inputs> | |
77 <outputs> | |
78 <data name="output" type="data" label="${tool.name} on ${on_string}" format="tabular" from_work_dir="out/confindr_report.csv" /> | |
79 </outputs> | |
80 <help><![CDATA[ | |
81 ]]></help> | |
82 <citations> | |
83 <citation type="bibtex"> | |
84 @misc{githubconfindr, | |
85 author = {Low,Andrew}, | |
86 year = {2018}, | |
87 title = {confindr}, | |
88 publisher = {GitHub}, | |
89 journal = {GitHub repository}, | |
90 url = {https://github.com/lowandrew/ConFindr}, | |
91 }</citation> | |
92 </citations> | |
93 </tool> |