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comparison shigatyper.xml @ 2:ce999a6ef3ba

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planemo upload
author jpayne
date Wed, 31 Jul 2019 11:57:03 -0400
parents 00c8dbe0549a
children 05691eb68d52
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1:4b327e1f39f3 2:ce999a6ef3ba
2 <description>Shigella genoserotyping</description> 2 <description>Shigella genoserotyping</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.5">shigatyper</requirement> 4 <requirement type="package" version="1.0.5">shigatyper</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 shigatyper -n "$input1.name" "$input1" "$input2" -vv > "$output1" 7 #if $reads.reads_select == 'collection'
8 #set forward=$reads.coll.forward
9 #set reverse=$reads.coll.reverse
10 #set name=$reads.coll.name
11 #else
12 #set name=$reads.coll.forward.name.split('_')[0]
13 #end if
14
15 shigatyper -n "$name" "$forward" "$reverse" -vv >
16
17 #if $reads.reads_select == 'collection'
18 ${serotype_from_collection}
19 #else
20 ${serotype_from_history}
21 #end if
8 ]]></command> 22 ]]></command>
9 <inputs> 23 <inputs>
10 <param type="data" name="input1" format="fastqsanger, fastqsanger.gz" /> 24 <conditional name="reads">
11 <param type="data" name="input2" format="fastqsanger, fastqsanger.gz" /> 25 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
26 <option value="collection">Paired collection from your history</option>
27 <option value="history">Two FASTQ datasets from your history</option>
28 </param>
29 <when value="collection">
30 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
31 </when>
32 <when value="history">
33 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
34 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
35 </when>
36 </conditional>
12 </inputs> 37 </inputs>
13 <outputs> 38 <outputs>
14 <data name="output1" label="Shigella serotype prediction" format="tabular" /> 39 <data label="${reads.coll.name} Shigella serotype determination" name="serotype_from_collection" format="sam">
40 <filter>reads['reads_select'] == 'collection'</filter>
41 </data>
42 <data label="${reads.forward.name.split('_')[0]} Shigella serotype determination" name="serotype_from_history" format="sam">
43 <filter>reads['reads_select'] == 'history'</filter>
44 </data>
15 </outputs> 45 </outputs>
16 <tests> 46 <tests>
17 <test> 47 <test>
18 <param name="input1" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/> 48 <param name="reads_select" value="history" />
19 <param name="input2" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/> 49 <param name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
20 <output name="output1" file="output.tabular"/> 50 <param name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
51 <output name="serotype_from_history" file="output.tabular"/>
52 </test>
53 <test>
54 <param name="reads_select" value="collection" />
55 <param name="coll">
56 <collection type="paired">
57 <element name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" />
58 <element name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" />
59 </collection>
60 </param>
61 <output name="serotype_from_collection" value="output.tabular" />
21 </test> 62 </test>
22 </tests> 63 </tests>
23 <help><![CDATA[ 64 <help><![CDATA[
24 usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2 65 usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2
25 66
30 71
31 ]]></help> 72 ]]></help>
32 <citations> 73 <citations>
33 <citation type="bibtex"> 74 <citation type="bibtex">
34 @misc{githubshigatyper, 75 @misc{githubshigatyper,
35 author = {LastTODO, FirstTODO}, 76 author = Wu Y1, Lau HK, Lee T, Lau DK, Payne J.
36 year = {TODO}, 77 year = 2019,
37 title = {shigatyper}, 78 title = In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification,
38 publisher = {GitHub}, 79 publisher = AEM,
39 journal = {GitHub repository}, 80 journal = Appl Environ Microbiol. ,
40 url = {https://github.com/CFSAN-Biostatistics/shigatyper}, 81 url = https://www.ncbi.nlm.nih.gov/pubmed/30709819,
41 }</citation> 82 }</citation>
42 </citations> 83 </citations>
43 </tool> 84 </tool>