Mercurial > repos > iuc > colibread_kissplice

comparison kissplice.xml @ 5:7d4435f9c77d draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author iuc
date Thu, 06 May 2021 12:44:17 +0000
parents d5b4404c4788
children
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4:ccc77612cbb9 5:7d4435f9c77d
1 <?xml version='1.0' encoding='utf-8'?> 1 <tool id="kissplice" name="KisSplice" version="2.4.0+galaxy0" profile="@PROFILE@">
2 <tool profile="16.04" id="kissplice" name="KisSplice" version="2.4.0">
3 <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>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <requirements> 6 <requirements>
8 <requirement type="package" version="2.4.0p1">kissplice</requirement> 7 <requirement type="package" version="2.4.0p1">kissplice</requirement>
9 </requirements> 8 </requirements>
10 <version_command>kissplice --version</version_command> 9 <version_command>kissplice --version</version_command>
11 <command><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
12
13 ## prepare symlinks
14 #set $samples = "" 11 #set $samples = ""
15 12 #for input in $list_reads
16 #for x in $list_reads 13 @single_reads@
17 #set $filename = os.path.basename(str($x)) + "." + $x.ext
18 ln -sf '${x}' '${filename}' &&
19 #set $samples += " -r '" + $filename + "'" 14 #set $samples += " -r '" + $filename + "'"
20 #end for 15 #end for
21
22 kissplice 16 kissplice
23 $samples 17 $samples
24 -k ${k} 18 -k ${k}
25 -c ${c} 19 -c ${c}
26 -C ${C} 20 -C ${C}
27 ${output_context} 21 ${output_context}
28 --counts ${counts} 22 --counts ${counts}
29
30 ]]></command> 23 ]]></command>
31 <inputs> 24 <inputs>
32 25 <param name='list_reads' argument="-r" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" type="data" label="Reads file" />
33 <param name='list_reads' argument="-r" multiple="true" format="fasta,fastq" type="data" label="Reads file" />
34 <param argument="-k" type="integer" value="41" label="K-mer length" /> 26 <param argument="-k" type="integer" value="41" label="K-mer length" />
35 <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)" />
36 <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)" />
37 <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 name="output_context" argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" />
38 <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">
61 </data> 53 </data>
62 <data name="type4" format="fasta" label="Other events" from_work_dir="results/*_coherents_type_4.fa"> 54 <data name="type4" format="fasta" label="Other events" from_work_dir="results/*_coherents_type_4.fa">
63 <filter>output_option == 'all_files'</filter> 55 <filter>output_option == 'all_files'</filter>
64 </data> 56 </data>
65 </outputs> 57 </outputs>
66
67 <tests> 58 <tests>
68 <test> 59 <test>
69 <param name="list_reads" value="kissplice/reads1,kissplice/reads2" ftype="fasta" /> 60 <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
70 <param name="k" value="25"/> 61 <param name="k" value="25"/>
71 <param name="output_option" value="alternative_file" /> 62 <param name="output_option" value="alternative_file" />
72 <output name="type1" file="kissplice/alternative_splicing.fa"/> 63 <output name="type1" file="kissplice/alternative_splicing.fa"/>
73 </test> 64 </test>
74 </tests> 65 </tests>
75
76 <help><![CDATA[ 66 <help><![CDATA[
77 67
78 **Description** 68 **Description**
79 69
80 KisSplice is a piece of software that enables the **analysis of RNA-seq data with or without a reference genome**. It is an exact local transcriptome assembler that allows one to identify **SNPs, indels and alternative splicing events**. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads. 70 KisSplice is a piece of software that enables the **analysis of RNA-seq data with or without a reference genome**. It is an exact local transcriptome assembler that allows one to identify **SNPs, indels and alternative splicing events**. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.