Mercurial > repos > lparsons > cutadapt
changeset 28:c053d4cad713 draft
"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 (2021-11-27) |
parents | de6cebe3c043 |
children | 48f587c13075 |
files | cutadapt.xml macros.xml |
diffstat | 2 files changed, 5 insertions(+), 7 deletions(-) [+] |
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--- a/cutadapt.xml Mon Nov 01 12:14:05 2021 +0000 +++ b/cutadapt.xml Sat Nov 27 10:09:14 2021 +0000 @@ -134,7 +134,7 @@ #if str($filter_options.max_expected_errors): --max-expected-errors=$filter_options.max_expected_errors #end if - +$filter_options.discard_cassava #if str($read_mod_options.quality_cutoff) != '0': --quality-cutoff=$read_mod_options.quality_cutoff @@ -143,6 +143,9 @@ --nextseq-trim=$read_mod_options.nextseq_trim #end if $read_mod_options.trim_n +#if $read_mod_options.strip_suffix != '' + --strip-suffix $read_mod_options.strip_suffix +#end if #if str($read_mod_options.shorten_options.shorten_values) == 'True': #if str($read_mod_options.shorten_options.shorten_end) == '3prime' --length=$read_mod_options.shorten_options.length @@ -505,11 +508,9 @@ </conditional> </repeat> </section> - <param name="output_filtering" value="filter"/> <section name="filter_options"> <param name="discard_trimmed" value="True"/> </section> - <param name="read_modification" value="none"/> <output name="out1" file="cutadapt_discard.out" ftype="fastq"/> <assert_command> <has_text text="--discard-trimmed"/> @@ -526,8 +527,6 @@ </conditional> </repeat> </section> - <param name="output_filtering" value="default"/> - <param name="read_modification" value="none"/> <param name="output_selector" value="rest_file,json_stats"/> <output name="out1" file="cutadapt_rest.out" ftype="fasta"/> <output name="json_stats" file="cutadapt_rest.json" ftype="json"/> @@ -545,7 +544,6 @@ </conditional> </repeat> </section> - <param name="read_modification" value="modify"/> <param name="nextseq_trim" value="20" /> <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/> </test>
--- a/macros.xml Mon Nov 01 12:14:05 2021 +0000 +++ b/macros.xml Sat Nov 27 10:09:14 2021 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.5</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@FASTQ_TYPES@">fastq.gz,fastq,fasta</token> <xml name="edam_ontology"> <edam_topics>