Mercurial > repos > iuc > colibread_takeabreak

comparison takeabreak.xml @ 6:22a263a450d0 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 12:46:24 +0000
parents b0e311ac462c
children
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5:8286fbe97349 6:22a263a450d0
1 <?xml version='1.0' encoding='utf-8'?> 1 <tool id="takeabreak" name="TakeABreak" version="1.1.2+galaxy0" profile="@PROFILE@">
2 <tool profile="16.04" id="takeabreak" name="TakeABreak" version="1.1.2">
3 <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>
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="1.1.2">takeabreak</requirement> 7 <requirement type="package" version="1.1.2">takeabreak</requirement>
9 </requirements> 8 </requirements>
10 <command><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 10 #if str($input_type_option.input_type) == "simple"
12 ## if single reads
13 #if str( $input_type_option.input_type ) == "simple"
14 #for $input in $input_type_option.reads 11 #for $input in $input_type_option.reads
15 #if $input 12 @single_reads@
16 #set $filename = os.path.basename(str($input)) + "." + $input.ext 13 echo "${filename}" >> input.fof &&
17 ln -sf '${input}' '${filename}' &&
18 echo "${filename}" >> input.fof &&
19 #end if
20 #end for 14 #end for
21 #else 15 #else
22 ## if paired reads in a list 16 #for $i, $list in enumerate($input_type_option.reads_lists)
23 #for $i, $list in enumerate( $input_type_option.reads_lists ) 17 #for $input in $list.list_reads
24 #for $read in $list.list_reads 18 @single_reads@
25 #set $filename = os.path.basename(str($read)) + "." + $read.ext
26 ln -sf '${read}' '${filename}' &&
27 echo "${filename}" >> "indiv_${i}.fof" && 19 echo "${filename}" >> "indiv_${i}.fof" &&
28 #end for 20 #end for
29 echo "indiv_${i}.fof" >> input.fof && 21 echo "indiv_${i}.fof" >> input.fof &&
30 #end for 22 #end for
31 #end if 23 #end if
32
33 TakeABreak 24 TakeABreak
34
35 -in input.fof 25 -in input.fof
36 -kmer-size ${kmer_size} 26 -kmer-size ${kmer_size}
37 -abundance-min '${abundance_min}' 27 -abundance-min '${abundance_min}'
38 -abundance-max ${abundance_max} 28 -abundance-max ${abundance_max}
39 -solidity-kind ${solidity_kind} 29 -solidity-kind ${solidity_kind}
40 -lct ${lct} 30 -lct ${lct}
41 -max-sim ${max_sim} 31 -max-sim ${max_sim}
42 -repeat ${repeat} 32 -repeat ${repeat}
43
44 ]]></command> 33 ]]></command>
45
46 <inputs> 34 <inputs>
47 <!-- Input data files -->
48 <conditional name="input_type_option"> 35 <conditional name="input_type_option">
49 <param name="input_type" type="select" label="Input option"> 36 <param name="input_type" type="select" label="Input option">
50 <option value="simple">one individual = one read </option> 37 <option value="simple">one individual = one read </option>
51 <option value="list">one individual = several reads</option> 38 <option value="list">one individual = several reads</option>
52 </param> 39 </param>
53 <when value="simple"> 40 <when value="simple">
54 <param name='reads' argument="-in" format="fasta,fastq" type="data" multiple="true" label="Single read files" optional="True" /> 41 <param name='reads' argument="-in" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" optional="True" />
55 </when> 42 </when>
56 <when value="list"> 43 <when value="list">
57 <repeat name="reads_lists" title="Individual" min="1"> 44 <repeat name="reads_lists" title="Individual" min="1">
58 <param name='list_reads' argument="-in" format="fasta,fastq" type="data_collection" collection_type="list" multiple="true" label="Individual read files list"/> 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"/>
59 </repeat> 46 </repeat>
60 </when> 47 </when>
61 </conditional> 48 </conditional>
62 <param name="kmer_size" argument="-kmer-size" type="integer" label="Length of the k-mers" value="31" help="Set the length of used kmers" /> 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" />
63 <param name="abundance_min" argument="-abundance-min" type="text" label="Minimal abundance threshold" value="auto" /> 50 <param name="abundance_min" argument="-abundance-min" type="text" label="Minimal abundance threshold" value="auto" />
64 <param name="abundance_max" argument="-abundance-max" type="integer" label="Maximal abundance threshold" value="2147483647" /> 51 <param name="abundance_max" argument="-abundance-max" type="integer" label="Maximal abundance threshold" value="2147483647" />
65
66 <param name="solidity_kind" argument="-solidity-kind" type="select" label="Way to consider a solid kmer with several input datasets" > 52 <param name="solidity_kind" argument="-solidity-kind" type="select" label="Way to consider a solid kmer with several input datasets" >
67 <option value="one">One</option> 53 <option value="one">One</option>
68 <option value="sum">Sum</option> 54 <option value="sum">Sum</option>
69 <option value="all">All</option> 55 <option value="all">All</option>
70 </param> 56 </param>
71
72 <param argument="-lct" type="integer" label="local complexity threshold" value="100" help="Local complexity threshold" /> 57 <param argument="-lct" type="integer" label="local complexity threshold" value="100" help="Local complexity threshold" />
73 <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" /> 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" />
74 <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" /> 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" />
75 </inputs> 60 </inputs>
76
77 <outputs> 61 <outputs>
78 <data format="fasta" name="inversion" from_work_dir="TakeABreak_*.fasta" label="Inversions with ${tool.name} on ${on_string}"/> 62 <data format="fasta" name="inversion" from_work_dir="TakeABreak_*.fasta" label="Inversions with ${tool.name} on ${on_string}"/>
79 </outputs> 63 </outputs>
80 <tests> 64 <tests>
81 <test> 65 <test>
82 <conditional name="input_type_option"> 66 <conditional name="input_type_option">
83 <param name="input_type" value="list" /> 67 <param name="input_type" value="list" />
84 <repeat name="reads_lists"> 68 <repeat name="reads_lists">
85 <param name="list_reads"> 69 <param name="list_reads">
86 <collection type="list"> 70 <collection type="list">
87 <element name="example_reads" value="takeabreak/toy_example_reads.fasta" ftype="fasta"/> 71 <element name="example_reads" value="takeabreak/toy_example_reads.fasta.gz" ftype="fasta.gz"/>
88 <element name="example_reads_with_inv" value="takeabreak/toy_example_with_inv_reads.fasta" ftype="fasta"/> 72 <element name="example_reads_with_inv" value="takeabreak/toy_example_with_inv_reads.fasta.gz" ftype="fasta.gz"/>
89 </collection> 73 </collection>
90 </param> 74 </param>
91 </repeat> 75 </repeat>
92 </conditional> 76 </conditional>
93 <output name="inversion" file="takeabreak/inversion_list.fasta"/> 77 <output name="inversion" file="takeabreak/inversion_list.fasta"/>
94 </test> 78 </test>
95 <test> 79 <test>
96 <conditional name="input_type_option"> 80 <conditional name="input_type_option">
97 <param name="input_type" value="simple" /> 81 <param name="input_type" value="simple" />
98 <param name="reads" value="takeabreak/toy_example_reads.fasta,takeabreak/toy_example_with_inv_reads.fasta" /> 82 <param name="reads" value="takeabreak/toy_example_reads.fasta.gz,takeabreak/toy_example_with_inv_reads.fasta.gz" />
99 </conditional> 83 </conditional>
100 <output name="inversion" file="takeabreak/inversion.fasta"/> 84 <output name="inversion" file="takeabreak/inversion.fasta"/>
101 </test> 85 </test>
102 </tests> 86 </tests>
103 <help><![CDATA[ 87 <help><![CDATA[