Mercurial > repos > iuc > colibread_kissplice

comparison kissplice.xml @ 6:7c02beb8ba3d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:54:14 +0000
parents 7d4435f9c77d
children
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5:7d4435f9c77d 6:7c02beb8ba3d
1 <tool id="kissplice" name="KisSplice" version="2.4.0+galaxy0" profile="@PROFILE@"> 1 <tool id="kissplice" name="KisSplice" version="2.4.0+galaxy1" profile="@PROFILE@">
2 <description>is a local transcriptome assembler for SNPs, indels and AS events</description> 2 <description>is a local transcriptome assembler for SNPs, indels and AS events</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
24 <inputs> 24 <inputs>
25 <param name='list_reads' argument="-r" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" type="data" label="Reads file" /> 25 <param name='list_reads' argument="-r" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" type="data" label="Reads file" />
26 <param argument="-k" type="integer" value="41" label="K-mer length" /> 26 <param argument="-k" type="integer" value="41" label="K-mer length" />
27 <param argument="-c" type="integer" value="2" label="K-mers present strictly less than this number of times in the dataset will be discarded (integer value required)" /> 27 <param argument="-c" type="integer" value="2" label="K-mers present strictly less than this number of times in the dataset will be discarded (integer value required)" />
28 <param argument="-C" type="float" value="0.05" label="Edges with relative coverage below this number are removed (value in [0,1) required)" /> 28 <param argument="-C" type="float" value="0.05" label="Edges with relative coverage below this number are removed (value in [0,1) required)" />
29 <param name="output_context" argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" /> 29 <param argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" />
30 <param argument="--counts" type="select" label="Selecting how the counts will be reported"> 30 <param argument="--counts" type="select" label="Selecting how the counts will be reported">
31 <option value="0">Total counts</option> 31 <option value="0">Total counts</option>
32 <option value="1">Counts on junctions</option> 32 <option value="1">Counts on junctions</option>
33 <option value="2">All counts</option> 33 <option value="2">All counts</option>
34 </param> 34 </param>
36 <option value="alternative_file">Generate only the Alternative Splicing file</option> 36 <option value="alternative_file">Generate only the Alternative Splicing file</option>
37 <option value="all_files">Generate all files</option> 37 <option value="all_files">Generate all files</option>
38 </param> 38 </param>
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <data name="type0a" format="fasta" label="Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa"> 41 <data name="type0a" format="fasta" label="${tool.name} on ${on_string}: Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa">
42 <filter>output_option == 'all_files'</filter> 42 <filter>output_option == 'all_files'</filter>
43 </data> 43 </data>
44 <data name="type0b" format="fasta" label="Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa"> 44 <data name="type0b" format="fasta" label="${tool.name} on ${on_string}: Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa">
45 <filter>output_option == 'all_files'</filter> 45 <filter>output_option == 'all_files'</filter>
46 </data> 46 </data>
47 <data name="type1" format="fasta" label="Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/> 47 <data name="type1" format="fasta" label="${tool.name} on ${on_string}: Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/>
48 <data name="type2" format="fasta" label="Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa"> 48 <data name="type2" format="fasta" label="${tool.name} on ${on_string}: Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa">
49 <filter>output_option == 'all_files'</filter> 49 <filter>output_option == 'all_files'</filter>
50 </data> 50 </data>
51 <data name="type3" format="fasta" label="Short indels" from_work_dir="results/*_coherents_type_3.fa"> 51 <data name="type3" format="fasta" label="${tool.name} on ${on_string}: Short indels" from_work_dir="results/*_coherents_type_3.fa">
52 <filter>output_option == 'all_files'</filter> 52 <filter>output_option == 'all_files'</filter>
53 </data> 53 </data>
54 <data name="type4" format="fasta" label="Other events" from_work_dir="results/*_coherents_type_4.fa"> 54 <data name="type4" format="fasta" label="${tool.name} on ${on_string}: Other events" from_work_dir="results/*_coherents_type_4.fa">
55 <filter>output_option == 'all_files'</filter> 55 <filter>output_option == 'all_files'</filter>
56 </data> 56 </data>
57 </outputs> 57 </outputs>
58 <tests> 58 <tests>
59 <test> 59 <test expect_num_outputs="1">
60 <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" /> 60 <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
61 <param name="k" value="25"/> 61 <param name="k" value="25"/>
62 <param name="output_option" value="alternative_file" /> 62 <param name="output_option" value="alternative_file" />
63 <output name="type1" file="kissplice/alternative_splicing.fa"/> 63 <output name="type1" file="kissplice/alternative_splicing.fa"/>
64 </test>
65 <test expect_num_outputs="6">
66 <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
67 <param name="k" value="25"/>
68 <param name="output_option" value="all_files" />
69 <output name="type0a">
70 <assert_contents>
71 <has_n_lines n="0"/>
72 </assert_contents>
73 </output>
74 <output name="type0b">
75 <assert_contents>
76 <has_n_lines n="0"/>
77 </assert_contents>
78 </output>
79 <output name="type1" file="kissplice/alternative_splicing.fa"/>
80 <output name="type2">
81 <assert_contents>
82 <has_n_lines n="0"/>
83 </assert_contents>
84 </output>
85 <output name="type3">
86 <assert_contents>
87 <has_n_lines n="0"/>
88 </assert_contents>
89 </output>
90 <output name="type4">
91 <assert_contents>
92 <has_n_lines n="0"/>
93 </assert_contents>
94 </output>
64 </test> 95 </test>
65 </tests> 96 </tests>
66 <help><![CDATA[ 97 <help><![CDATA[
67 98
68 **Description** 99 **Description**
80 .. _here: http://kissplice.prabi.fr/ 111 .. _here: http://kissplice.prabi.fr/
81 112
82 113
83 ]]></help> 114 ]]></help>
84 <expand macro="citations"> 115 <expand macro="citations">
85 <citation type="bibtex"> 116 <citation type="doi">10.1186/1471-2105-13-S6-S5</citation>
86 @article{PMID:22537044,
87 author = {Sacomoto, G. A. and Kielbassa, J. and Chikhi, R. and Uricaru, R. and Antoniou, P. and Sagot, M. F. and Peterlongo, P. and Lacroix, V.},
88 title = {KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.},
89 journal = {BMC Bioinformatics},
90 year = {2012},
91 volume = {13 Suppl 6},
92 pages = {S5},
93 url = {http://www.ncbi.nlm.nih.gov/pubmed/22537044},
94 }
95 </citation>
96 </expand> 117 </expand>
97 118
98 </tool> 119 </tool>