Mercurial > repos > iuc > adapter_removal

comparison adapter_removal.xml @ 1:0a355925c1bf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit faa8c4bf004428988500537078264968ae05fa67
author iuc
date Mon, 26 Aug 2024 13:47:45 +0000
parents e42205a5495e
children
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0:e42205a5495e 1:0a355925c1bf
48 48
49 ###### FASTQ Options 49 ###### FASTQ Options
50 --qualitybase '33' 50 --qualitybase '33'
51 --qualitybase-output '33' 51 --qualitybase-output '33'
52 --qualitymax $fastq_options.qualitymax 52 --qualitymax $fastq_options.qualitymax
53 $fastq_options.convert_uracils
54 $fastq_options.mask_degenerate_bases
53 55
54 ###### FASTQ Trimming Options 56 ###### FASTQ Trimming Options
55 --adapter1 '$fastq_trimming_options.adapter1' 57 --adapter1 '$fastq_trimming_options.adapter1'
56 --adapter2 '$fastq_trimming_options.adapter2' 58 --adapter2 '$fastq_trimming_options.adapter2'
57 #if $fastq_trimming_options.adapter_list: 59 #if $fastq_trimming_options.adapter_list:
141 </when> 143 </when>
142 </conditional> 144 </conditional>
143 <!-- FASTQ Options --> 145 <!-- FASTQ Options -->
144 <section name="fastq_options" title="FASTQ Options" expanded="false"> 146 <section name="fastq_options" title="FASTQ Options" expanded="false">
145 <param argument="--qualitymax" type="integer" value="41" min="0" max="93" label="Maximum Phred score expected in input files and used when writing output files" help="Possible values are 0 to 93 for Phred+33 encoded files"/> 147 <param argument="--qualitymax" type="integer" value="41" min="0" max="93" label="Maximum Phred score expected in input files and used when writing output files" help="Possible values are 0 to 93 for Phred+33 encoded files"/>
148 <param argument="--mask-degenerate-bases" type="boolean" truevalue="--mask-degenerate-bases" falsevalue="" checked="false" label="Mask degenerate/ambiguous bases (B/D/H/K/M/N/R/S/V/W/Y)" help="This option will replace 'N's; if this option is not used, AdapterRemoval will abort upon encountering degenerate bases."/>
149 <param argument="--convert-uracils" type="boolean" truevalue="--convert-uracils" falsevalue="" checked="false" label="Convert uracils (U) to thymine (T) " help="If this option is not used, AdapterRemoval will abort upon encountering uracils."/>
146 </section> 150 </section>
147 <!-- FASTQ Trimming Options --> 151 <!-- FASTQ Trimming Options -->
148 <section name="fastq_trimming_options" title="FASTQ Trimming Options" expanded="false"> 152 <section name="fastq_trimming_options" title="FASTQ Trimming Options" expanded="false">
149 <param argument="--adapter1" type="text" value="AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG" label="Adapter sequence expected to be found in mate 1 reads, specified in read direction"> 153 <param argument="--adapter1" type="text" value="AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG" label="Adapter sequence expected to be found in mate 1 reads, specified in read direction">
150 <expand macro="sanitizer"/> 154 <expand macro="sanitizer"/>
263 <!-- Dataset pair input, all defaults --> 267 <!-- Dataset pair input, all defaults -->
264 <test expect_num_outputs="3"> 268 <test expect_num_outputs="3">
265 <param name="input_type" value="pair"/> 269 <param name="input_type" value="pair"/>
266 <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/> 270 <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
267 <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/> 271 <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
272 <section name="fastq_options">
273 <param name="convert_uracils" value="false"/>
274 <param name="mask_degenerate_bases" value="true"/>
275 </section>
268 <output name="output_settings" ftype="txt"> 276 <output name="output_settings" ftype="txt">
269 <assert_contents> 277 <assert_contents>
270 <has_size value="2594" delta="10"/> 278 <has_size value="2594" delta="10"/>
271 </assert_contents> 279 </assert_contents>
272 <assert_contents> 280 <assert_contents>