Mercurial > repos > iuc > colibread_takeabreak

comparison takeabreak.xml @ 7:1339a2bb75ce 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 19:54:32 +0000
parents 22a263a450d0
children
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6:22a263a450d0 7:1339a2bb75ce
1 <tool id="takeabreak" name="TakeABreak" version="1.1.2+galaxy0" profile="@PROFILE@"> 1 <tool id="takeabreak" name="TakeABreak" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>is a tool that can detect inversion breakpoints directly from raw NGS reads</description> 2 <description>is a tool that can detect inversion breakpoints directly from raw NGS reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.1.2</token>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="1.1.2">takeabreak</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">takeabreak</requirement>
8 </requirements> 9 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 #if str($input_type_option.input_type) == "simple" 11 #if str($input_type_option.input_type) == "simple"
11 #for $input in $input_type_option.reads 12 #for $input in $input_type_option.reads
12 @single_reads@ 13 @single_reads@
44 <repeat name="reads_lists" title="Individual" min="1"> 45 <repeat name="reads_lists" title="Individual" min="1">
45 <param name='list_reads' argument="-in" format="fasta,fasta.gz,fastqfastq.gz" type="data_collection" collection_type="list" multiple="true" label="Individual read files list"/> 46 <param name='list_reads' argument="-in" format="fasta,fasta.gz,fastqfastq.gz" type="data_collection" collection_type="list" multiple="true" label="Individual read files list"/>
46 </repeat> 47 </repeat>
47 </when> 48 </when>
48 </conditional> 49 </conditional>
49 <param name="kmer_size" argument="-kmer-size" type="integer" label="Length of the k-mers" value="31" help="Set the length of used kmers" /> 50 <param argument="-kmer-size" type="integer" label="Length of the k-mers" value="31" help="Set the length of used kmers" />
50 <param name="abundance_min" argument="-abundance-min" type="text" label="Minimal abundance threshold" value="auto" /> 51 <param argument="-abundance-min" type="text" label="Minimal abundance threshold" value="auto" />
51 <param name="abundance_max" argument="-abundance-max" type="integer" label="Maximal abundance threshold" value="2147483647" /> 52 <param argument="-abundance-max" type="integer" label="Maximal abundance threshold" value="2147483647" />
52 <param name="solidity_kind" argument="-solidity-kind" type="select" label="Way to consider a solid kmer with several input datasets" > 53 <param argument="-solidity-kind" type="select" label="Way to consider a solid kmer with several input datasets" >
53 <option value="one">One</option> 54 <option value="one">One</option>
54 <option value="sum">Sum</option> 55 <option value="sum">Sum</option>
55 <option value="all">All</option> 56 <option value="all">All</option>
56 </param> 57 </param>
57 <param argument="-lct" type="integer" label="local complexity threshold" value="100" help="Local complexity threshold" /> 58 <param argument="-lct" type="integer" label="local complexity threshold" value="100" help="Local complexity threshold" />
58 <param name="max_sim" argument="-max-sim" type="integer" label="max similarity percentage" value="80" help="Inversions with a and b' (or u and v') whose longest common subsequence size is bigger than k*(this value)/100 are discarded" /> 59 <param argument="-max-sim" type="integer" label="max similarity percentage" value="80" help="Inversions with a and b' (or u and v') whose longest common subsequence size is bigger than k*(this value)/100 are discarded" />
59 <param argument="-repeat" type="integer" label="maximal repeat size" value="8" help="Maximal repeat size at the breakpoint. Longest common suffix between a and b" /> 60 <param argument="-repeat" type="integer" label="maximal repeat size" value="8" help="Maximal repeat size at the breakpoint. Longest common suffix between a and b" />
60 </inputs> 61 </inputs>
61 <outputs> 62 <outputs>
62 <data format="fasta" name="inversion" from_work_dir="TakeABreak_*.fasta" label="Inversions with ${tool.name} on ${on_string}"/> 63 <data format="fasta" name="inversion" from_work_dir="TakeABreak_*.fasta" label="${tool.name} on ${on_string}: Inversions"/>
63 </outputs> 64 </outputs>
64 <tests> 65 <tests>
65 <test> 66 <test>
66 <conditional name="input_type_option"> 67 <conditional name="input_type_option">
67 <param name="input_type" value="list" /> 68 <param name="input_type" value="list" />