Mercurial > repos > lparsons > cutadapt

comparison cutadapt.xml @ 28:c053d4cad713 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 9ec830a98da45d5fb2f92a817c7cd0376504be90"
author iuc
date Sat, 27 Nov 2021 10:09:14 +0000
parents de6cebe3c043
children 48f587c13075
comparison
equal deleted inserted replaced
27:de6cebe3c043 28:c053d4cad713
132 #end if 132 #end if
133 #end if 133 #end if
134 #if str($filter_options.max_expected_errors): 134 #if str($filter_options.max_expected_errors):
135 --max-expected-errors=$filter_options.max_expected_errors 135 --max-expected-errors=$filter_options.max_expected_errors
136 #end if 136 #end if
137 137 $filter_options.discard_cassava
138 138
139 #if str($read_mod_options.quality_cutoff) != '0': 139 #if str($read_mod_options.quality_cutoff) != '0':
140 --quality-cutoff=$read_mod_options.quality_cutoff 140 --quality-cutoff=$read_mod_options.quality_cutoff
141 #end if 141 #end if
142 #if str($read_mod_options.nextseq_trim) != '0': 142 #if str($read_mod_options.nextseq_trim) != '0':
143 --nextseq-trim=$read_mod_options.nextseq_trim 143 --nextseq-trim=$read_mod_options.nextseq_trim
144 #end if 144 #end if
145 $read_mod_options.trim_n 145 $read_mod_options.trim_n
146 #if $read_mod_options.strip_suffix != ''
147 --strip-suffix $read_mod_options.strip_suffix
148 #end if
146 #if str($read_mod_options.shorten_options.shorten_values) == 'True': 149 #if str($read_mod_options.shorten_options.shorten_values) == 'True':
147 #if str($read_mod_options.shorten_options.shorten_end) == '3prime' 150 #if str($read_mod_options.shorten_options.shorten_end) == '3prime'
148 --length=$read_mod_options.shorten_options.length 151 --length=$read_mod_options.shorten_options.length
149 #else 152 #else
150 --length=-$read_mod_options.shorten_options.length 153 --length=-$read_mod_options.shorten_options.length
503 <param name="adapter_source_list" value="user"/> 506 <param name="adapter_source_list" value="user"/>
504 <param name="adapter" value="TTAGACATATCTCCGTCG"/> 507 <param name="adapter" value="TTAGACATATCTCCGTCG"/>
505 </conditional> 508 </conditional>
506 </repeat> 509 </repeat>
507 </section> 510 </section>
508 <param name="output_filtering" value="filter"/>
509 <section name="filter_options"> 511 <section name="filter_options">
510 <param name="discard_trimmed" value="True"/> 512 <param name="discard_trimmed" value="True"/>
511 </section> 513 </section>
512 <param name="read_modification" value="none"/>
513 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/> 514 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
514 <assert_command> 515 <assert_command>
515 <has_text text="--discard-trimmed"/> 516 <has_text text="--discard-trimmed"/>
516 </assert_command> 517 </assert_command>
517 </test> 518 </test>
524 <param name="adapter_source_list" value="user"/> 525 <param name="adapter_source_list" value="user"/>
525 <param name="adapter" value="AAAGATG"/> 526 <param name="adapter" value="AAAGATG"/>
526 </conditional> 527 </conditional>
527 </repeat> 528 </repeat>
528 </section> 529 </section>
529 <param name="output_filtering" value="default"/>
530 <param name="read_modification" value="none"/>
531 <param name="output_selector" value="rest_file,json_stats"/> 530 <param name="output_selector" value="rest_file,json_stats"/>
532 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/> 531 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
533 <output name="json_stats" file="cutadapt_rest.json" ftype="json"/> 532 <output name="json_stats" file="cutadapt_rest.json" ftype="json"/>
534 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/> 533 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
535 </test> 534 </test>
543 <param name="adapter_source_list" value="user"/> 542 <param name="adapter_source_list" value="user"/>
544 <param name="adapter" value="AGATCGGAAGAGC"/> 543 <param name="adapter" value="AGATCGGAAGAGC"/>
545 </conditional> 544 </conditional>
546 </repeat> 545 </repeat>
547 </section> 546 </section>
548 <param name="read_modification" value="modify"/>
549 <param name="nextseq_trim" value="20" /> 547 <param name="nextseq_trim" value="20" />
550 <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/> 548 <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
551 </test> 549 </test>
552 <!-- Ensure Report and Info file output work --> 550 <!-- Ensure Report and Info file output work -->
553 <test expect_num_outputs="3"> 551 <test expect_num_outputs="3">