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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop commit f04670edc196c683e09beb1fc1d8bc731162d47f
author iuc
date Sun, 09 Feb 2025 20:38:35 +0000
parents 543cbeef3949
children
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3:543cbeef3949 4:a2899db6bd6e
1 <tool id="porechop" name="Porechop" version="@WRAPPER_VERSION@+galaxy0" profile="20.01"> 1 <tool id="porechop" name="Porechop" version="@WRAPPER_VERSION@+galaxy1" profile="20.01">
2 <description>adapter trimmer for Oxford Nanopore reads</description> 2 <description>adapter trimmer for Oxford Nanopore reads</description>
3 <macros> 3 <macros>
4 <token name="@WRAPPER_VERSION@">0.2.4</token> 4 <token name="@WRAPPER_VERSION@">0.2.4</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@WRAPPER_VERSION@">porechop</requirement> 7 <requirement type="package" version="@WRAPPER_VERSION@">porechop</requirement>
8 </requirements> 8 </requirements>
9 <version_command>porechop --version</version_command> 9 <version_command>porechop --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #import re
12
13 #set file_path = re.sub('[^\s\w\-.]', '_', str($input_file.element_identifier))
14
15 ln -s '$input_file' '$file_path' &&
16
11 porechop 17 porechop
12 -i '$input_file' 18 -i '$file_path'
13 --format '$format' 19 --format '$format'
14 --barcode_threshold '$barcode_binning_settings.barcode_threshold' 20 --barcode_threshold '$barcode_binning_settings.barcode_threshold'
15 --barcode_diff '$barcode_binning_settings.barcode_diff' 21 --barcode_diff '$barcode_binning_settings.barcode_diff'
16 $barcode_binning_settings.require_two_barcodes 22 $barcode_binning_settings.require_two_barcodes
17 $barcode_binning_settings.discard_unassigned 23 $barcode_binning_settings.discard_unassigned
27 --middle_threshold '$middle_adapter_settings.middle_threshold' 33 --middle_threshold '$middle_adapter_settings.middle_threshold'
28 --extra_middle_trim_good_side '$middle_adapter_settings.extra_middle_trim_good_side' 34 --extra_middle_trim_good_side '$middle_adapter_settings.extra_middle_trim_good_side'
29 --extra_middle_trim_bad_side '$middle_adapter_settings.extra_middle_trim_bad_side' 35 --extra_middle_trim_bad_side '$middle_adapter_settings.extra_middle_trim_bad_side'
30 --min_split_read_size '$middle_adapter_settings.min_split_read_size' 36 --min_split_read_size '$middle_adapter_settings.min_split_read_size'
31 -o 'out.$format' 37 -o 'out.$format'
38 #if $log_file
39 > '$log_output'
40 #end if
32 41
33 ]]></command> 42 ]]></command>
34 <inputs> 43 <inputs>
35 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" /> 44 <param name="input_file" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Input FASTA/FASTQ" help="FASTA/FASTQ of input reads" />
36 <param name="format" type="select" label="Output format for the reads" help="Output format for the reads"> 45 <param name="format" type="select" label="Output format for the reads" help="Output format for the reads">
81 <param argument="--extra_middle_trim_bad_side" type="integer" min="0" value="100" optional="True" label="Extra trimming bad side" 90 <param argument="--extra_middle_trim_bad_side" type="integer" min="0" value="100" optional="True" label="Extra trimming bad side"
82 help="This many additional bases will be removed next to middle adapters on their 'bad' side (default: 100)"/> 91 help="This many additional bases will be removed next to middle adapters on their 'bad' side (default: 100)"/>
83 <param argument="--min_split_read_size" type="integer" min="0" value="1000" optional="True" label="Minimum length reads post-split" 92 <param argument="--min_split_read_size" type="integer" min="0" value="1000" optional="True" label="Minimum length reads post-split"
84 help="Post-split read pieces smaller than this many base pairs will not be outputted (default: 1000)"/> 93 help="Post-split read pieces smaller than this many base pairs will not be outputted (default: 1000)"/>
85 </section> 94 </section>
95 <param name="log_file" type="boolean" label="Generate log file" help="Generates a log file out of stdout, which can be used as MultiQC input"/>
86 </inputs> 96 </inputs>
87 <outputs> 97 <outputs>
88 <data name="outfile" format="fasta" from_work_dir="out.*" label="${tool.name} on ${on_string}: Trimmed"> 98 <data name="outfile" format="fasta" from_work_dir="out.*" label="${tool.name} on ${on_string}: Trimmed">
89 <change_format> 99 <change_format>
90 <when input="format" value="fastq" format="fastqsanger"/> 100 <when input="format" value="fastq" format="fastqsanger"/>
91 <when input="format" value="fasta.gz" format="fasta.gz"/> 101 <when input="format" value="fasta.gz" format="fasta.gz"/>
92 <when input="format" value="fastq.gz" format="fastqsanger.gz"/> 102 <when input="format" value="fastq.gz" format="fastqsanger.gz"/>
93 </change_format> 103 </change_format>
94 </data> 104 </data>
105 <data name="log_output" format="txt" label="Porechop log file">
106 <filter>log_file</filter>
107 </data>
95 </outputs> 108 </outputs>
96 <tests> 109 <tests>
97 <test> 110 <test expect_num_outputs="2">
98 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 111 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
99 <param name="format" value="fasta"/> 112 <param name="format" value="fasta"/>
113 <param name="log_file" value="true"/>
100 <output name="outfile" ftype="fasta" file="out.fasta"/> 114 <output name="outfile" ftype="fasta" file="out.fasta"/>
115 <output name="log_output" ftype="txt">
116 <assert_contents>
117 <has_line line=" PCR adapters 2 66.7 63.6"/>
118 <has_line line=" Barcode 1 (reverse) 59.4 66.7"/>
119 <has_line line="4 / 9 reads had adapters trimmed from their start (74 bp removed)"/>
120 <has_line line="3 / 9 reads had adapters trimmed from their end (49 bp removed)"/>
121 </assert_contents>
122 </output>
101 </test> 123 </test>
102 <test> 124 <test expect_num_outputs="1">
103 <param name="input_file" ftype="fastqsanger.gz" value="test_format.fastq.gz"/> 125 <param name="input_file" ftype="fastqsanger.gz" value="test_format.fastq.gz"/>
104 <param name="format" value="fastq"/> 126 <param name="format" value="fastq"/>
105 <output name="outfile" ftype="fastqsanger" file="out.fastq"/> 127 <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
106 </test> 128 </test>
107 <test> 129 <test expect_num_outputs="1">
108 <param name="input_file" ftype="fastq.gz" value="test_format.fastq.gz"/> 130 <param name="input_file" ftype="fastq.gz" value="test_format.fastq.gz"/>
109 <param name="format" value="fastq"/> 131 <param name="format" value="fastq"/>
110 <output name="outfile" ftype="fastqsanger" file="out.fastq"/> 132 <output name="outfile" ftype="fastqsanger" file="out.fastq"/>
111 </test> 133 </test>
112 <test> 134 <test expect_num_outputs="1">
113 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 135 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
114 <param name="format" value="fasta.gz"/> 136 <param name="format" value="fasta.gz"/>
115 <output name="outfile" ftype="fasta.gz" file="out.fasta.gz" compare="sim_size"/> 137 <output name="outfile" ftype="fasta.gz" file="out.fasta.gz" compare="sim_size"/>
116 </test> 138 </test>
117 <test> 139 <test expect_num_outputs="1">
118 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 140 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
119 <param name="format" value="fastq.gz"/> 141 <param name="format" value="fastq.gz"/>
120 <output name="outfile" ftype="fastqsanger.gz" file="out.fastq.gz" compare="sim_size"/> 142 <output name="outfile" ftype="fastqsanger.gz" file="out.fastq.gz" compare="sim_size"/>
121 </test> 143 </test>
122 <test> 144 <test expect_num_outputs="1">
123 <param name="input_file" ftype="fasta" value="test_format.fasta"/> 145 <param name="input_file" ftype="fasta" value="test_format.fasta"/>
124 <param name="format" value="fasta"/> 146 <param name="format" value="fasta"/>
125 <param name="barcode_threshold" value="70"/> 147 <param name="barcode_threshold" value="70"/>
126 <param name="barcode_diff" value="4"/> 148 <param name="barcode_diff" value="4"/>
127 <param name="require_two_barcodes" value="True"/> 149 <param name="require_two_barcodes" value="True"/>
130 <param name="min_trim_size" value="2"/> 152 <param name="min_trim_size" value="2"/>
131 <param name="extra_end_trim" value="1"/> 153 <param name="extra_end_trim" value="1"/>
132 <param name="end_threshold" value="80"/> 154 <param name="end_threshold" value="80"/>
133 <param name="discard_middle" value="True"/> 155 <param name="discard_middle" value="True"/>
134 <param name="middle_threshold" value="90"/> 156 <param name="middle_threshold" value="90"/>
135 <param name="extra_middle_trim_good_size" value="3"/> 157 <param name="extra_middle_trim_good_side" value="3"/>
136 <param name="extra_middle_trim_bad_size" value="30"/> 158 <param name="extra_middle_trim_bad_side" value="30"/>
137 <param name="min_split_read_size" value="1500"/> 159 <param name="min_split_read_size" value="1500"/>
138 <output name="outfile" ftype="fasta" file="out_advanced.fasta"/> 160 <output name="outfile" ftype="fasta" file="out_advanced.fasta"/>
139 </test> 161 </test>
140 </tests> 162 </tests>
141 <help><![CDATA[ 163 <help><![CDATA[