Mercurial > repos > iuc > colibread_lordec

comparison lordec.xml @ 6:434af4cbf682 draft

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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 12:39:45 +0000
parents 87c61a0e1177
children 552041078feb
comparison
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5:87c61a0e1177 6:434af4cbf682
1 <?xml version='1.0' encoding='utf-8'?> 1 <tool id="lordec" name="Lordec" version="0.9+galaxy2" profile="@PROFILE@">
2 <tool profile="16.04" id="lordec" name="Lordec" version="0.9+galaxy1">
3 <description>is a set a programs for correcting sequencing errors in PacBio reads</description> 2 <description>is a set a programs for correcting sequencing errors in PacBio 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="0.9">lordec</requirement> 7 <requirement type="package" version="0.9">lordec</requirement>
9 </requirements> 8 </requirements>
10 <command><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 10 #if str( $program_type_choice.program_type ) == "correct":
12 #if str( $program_type_choice.program_type ) == "correct"
13 lordec-correct 11 lordec-correct
14 @lordec_inputs@ 12 @lordec_inputs@
15 #if str( $program_type_choice.advanced_options.advanced_options_selector ) == "advanced" 13 #if str( $program_type_choice.advanced_options.advanced_options_selector ) == "advanced":
16 -t ${program_type_choice.advanced_options.t} 14 -t ${program_type_choice.advanced_options.t}
17 -b ${program_type_choice.advanced_options.b} 15 -b ${program_type_choice.advanced_options.b}
18 -e ${program_type_choice.advanced_options.e} 16 -e ${program_type_choice.advanced_options.e}
19 #end if 17 #end if
20 -T \${GALAXY_SLOTS:-1} 18 -T \${GALAXY_SLOTS:-1}
21 -o '${corrected_read_file}' 19 -o '${corrected_read_file}'
22 20 #else if str( $program_type_choice.program_type ) == "trim":
23
24 #else if str( $program_type_choice.program_type ) == "trim"
25 #if $program_type_choice.split 21 #if $program_type_choice.split
26 lordec-trim-split 22 lordec-trim-split
27 #else 23 #else
28 lordec-trim 24 lordec-trim
29 #end if 25 #end if
30 -i '${program_type_choice.i}' 26 -i '${program_type_choice.i}'
31 -o '${trimmed_reads_file}' 27 -o '${trimmed_reads_file}'
32
33 #else 28 #else
34 lordec-stat 29 lordec-stat
35 @lordec_inputs@ 30 @lordec_inputs@
36 -S '${stat_file}' 31 -S '${stat_file}'
37 #end if 32 #end if
38
39
40 ]]></command> 33 ]]></command>
41
42 <inputs> 34 <inputs>
43
44 <conditional name="program_type_choice"> 35 <conditional name="program_type_choice">
45 <param name="program_type" type="select" label="Choose Lordec program"> 36 <param name="program_type" type="select" label="Choose Lordec program">
46 <option value="correct">Lordec Correct</option> 37 <option value="correct">Lordec Correct</option>
47 <option value="trim">Lordec Trim</option> 38 <option value="trim">Lordec Trim</option>
48 <option value="stats">Lordec Statistics</option> 39 <option value="stats">Lordec Statistics</option>
49 </param> 40 </param>
50
51 <when value="correct"> 41 <when value="correct">
52 <expand macro="lordec_inputs" /> 42 <expand macro="lordec_inputs" />
53 <conditional name="advanced_options"> 43 <conditional name="advanced_options">
54 <param name="advanced_options_selector" type="select" label="Lordec correct advanced options"> 44 <param name="advanced_options_selector" type="select" label="Lordec correct advanced options">
55 <option value="default" selected="true">Default</option> 45 <option value="default" selected="true">Default</option>
61 <param argument="-b" type="integer" label="Maximum number of branches to explore" value="200" /> 51 <param argument="-b" type="integer" label="Maximum number of branches to explore" value="200" />
62 <param argument="-e" type="float" label="Maximum error rate" value="0.4" /> 52 <param argument="-e" type="float" label="Maximum error rate" value="0.4" />
63 </when> 53 </when>
64 </conditional> 54 </conditional>
65 </when> 55 </when>
66
67 <when value="trim"> 56 <when value="trim">
68 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" /> 57 <param argument="-i" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Long read FASTA/Q file" help="PacBio reads files" />
69 <param name="split" type="boolean" label="Use the split option" help="Trim all weak regions and split the reads on inner weak regions" /> 58 <param name="split" type="boolean" label="Use the split option" help="Trim all weak regions and split the reads on inner weak regions" />
70 </when> 59 </when>
71
72 <when value="stats"> 60 <when value="stats">
73 <expand macro="lordec_inputs" /> 61 <expand macro="lordec_inputs" />
74 </when> 62 </when>
75
76 </conditional> 63 </conditional>
77
78 </inputs> 64 </inputs>
79
80 <outputs> 65 <outputs>
81 <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" > 66 <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" >
82 <filter>program_type_choice['program_type'] == 'correct'</filter> 67 <filter>program_type_choice['program_type'] == 'correct'</filter>
83 </data> 68 </data>
84 <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" > 69 <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" >
86 </data> 71 </data>
87 <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" > 72 <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" >
88 <filter>program_type_choice['program_type'] == 'stats'</filter> 73 <filter>program_type_choice['program_type'] == 'stats'</filter>
89 </data> 74 </data>
90 </outputs> 75 </outputs>
91
92 <tests> 76 <tests>
93 <test> 77 <test>
94 <conditional name="program_type_choice"> 78 <conditional name="program_type_choice">
95 <param name="program_type" value="correct" /> 79 <param name="program_type" value="correct" />
96 <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" /> 80 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" ftype="fasta.gz"/>
97 <param name="i" value="lordec/coli-pacbio-test-mini.fa" /> 81 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
98 <param name="k" value="31" /> 82 <param name="k" value="31" />
99 </conditional> 83 </conditional>
100 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/> 84 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/>
101 </test> 85 </test>
102 <test> 86 <test>
103 <conditional name="program_type_choice"> 87 <conditional name="program_type_choice">
104 <param name="program_type" value="trim" /> 88 <param name="program_type" value="trim" />
105 <param name="i" value="lordec/corrected_reads.fa" /> 89 <param name="i" value="lordec/corrected_reads.fa" ftype="fasta"/>
106 </conditional> 90 </conditional>
107 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/> 91 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/>
108 </test> 92 </test>
109 <test> 93 <test>
110 <conditional name="program_type_choice"> 94 <conditional name="program_type_choice">
111 <param name="program_type" value="stats" /> 95 <param name="program_type" value="stats" />
112 <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" /> 96 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" />
113 <param name="i" value="lordec/coli-pacbio-test-mini.fa" /> 97 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
114 </conditional> 98 </conditional>
115 <output name="stat_file" file="lordec/stat_file.txt" compare="sim_size" delta="10"/> 99 <output name="stat_file" file="lordec/stat_file.txt" compare="sim_size" delta="10"/>
116 </test> 100 </test>
117 </tests> 101 </tests>
118 <help><![CDATA[ 102 <help><![CDATA[