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comparison cutadapt.xml @ 22:093678460093 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
author iuc
date Sat, 04 Jul 2020 06:52:59 -0400
parents 104d86c98776
children c4b82dce8335
comparison
equal deleted inserted replaced
21:104d86c98776 22:093678460093
1 <tool id="cutadapt" name="Cutadapt" version="1.16.7" profile="17.09"> 1 <tool id="cutadapt" name="Cutadapt" version="1.16.8" profile="17.09">
2 <description>Remove adapter sequences from Fastq/Fasta</description> 2 <description>Remove adapter sequences from Fastq/Fasta</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
111 --minimum-length=$filter_options.min 111 --minimum-length=$filter_options.min
112 #end if 112 #end if
113 #if str($filter_options.max): 113 #if str($filter_options.max):
114 --maximum-length=$filter_options.max 114 --maximum-length=$filter_options.max
115 #end if 115 #end if
116 #if $filter_options.max_n: 116 #if str($filter_options.max_n):
117 --max-n=$filter_options.max_n 117 --max-n=$filter_options.max_n
118 #end if 118 #end if
119 #if str( $library.type ) != "single": 119 #if str( $library.type ) != "single":
120 #if $filter_options.pair_filter: 120 #if $filter_options.pair_filter:
121 --pair-filter=$filter_options.pair_filter 121 --pair-filter=$filter_options.pair_filter
129 #if str($read_mod_options.nextseq_trim) != '0': 129 #if str($read_mod_options.nextseq_trim) != '0':
130 --nextseq-trim=$read_mod_options.nextseq_trim 130 --nextseq-trim=$read_mod_options.nextseq_trim
131 #end if 131 #end if
132 $read_mod_options.trim_n 132 $read_mod_options.trim_n
133 #if $read_mod_options.prefix != '': 133 #if $read_mod_options.prefix != '':
134 --prefix="$read_mod_options.prefix" 134 --prefix='$read_mod_options.prefix'
135 #end if 135 #end if
136 #if $read_mod_options.suffix != '': 136 #if $read_mod_options.suffix != '':
137 --suffix="$read_mod_options.suffix" 137 --suffix='$read_mod_options.suffix'
138 #end if 138 #end if
139 #if str($read_mod_options.length) != '0': 139 #if str($read_mod_options.length) != '0':
140 --length=$read_mod_options.length 140 --length=$read_mod_options.length
141 #end if 141 #end if
142 #if $read_mod_options.length_tag != '': 142 #if $read_mod_options.length_tag != '':
143 --length-tag="$read_mod_options.length_tag" 143 --length-tag='$read_mod_options.length_tag'
144 #end if 144 #end if
145 145
146 '${read1}' 146 '${read1}'
147 #if $paired: 147 #if $paired:
148 '${read2}' 148 '${read2}'
516 <param name="adapter2" value="AGATCGGAAGAGC"/> 516 <param name="adapter2" value="AGATCGGAAGAGC"/>
517 <section name="filter_options"> 517 <section name="filter_options">
518 <param name="discard_untrimmed" value="true"/> 518 <param name="discard_untrimmed" value="true"/>
519 <param name="min" value="1"/> 519 <param name="min" value="1"/>
520 <param name="max" value="1000"/> 520 <param name="max" value="1000"/>
521 <param name="max_n" value="1"/> 521 <param name="max_n" value="0"/>
522 <param name="pair_filter" value="both"/> 522 <param name="pair_filter" value="both"/>
523 </section> 523 </section>
524 <assert_command> 524 <assert_command>
525 <has_text text="--discard-untrimmed"/> 525 <has_text text="--discard-untrimmed"/>
526 <has_text text="--minimum-length=1"/> 526 <has_text text="--minimum-length=1"/>
527 <has_text text="--maximum-length=1000"/> 527 <has_text text="--maximum-length=1000"/>
528 <has_text text="--max-n=1"/> 528 <has_text text="--max-n=0"/>
529 <has_text text="--pair-filter=both"/> 529 <has_text text="--pair-filter=both"/>
530 </assert_command> 530 </assert_command>
531 </test> 531 </test>
532 </tests> 532 </tests>
533 533