Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_cutadapt_trim-paired.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_cutadapt_trim-paired.xml Fri Sep 04 13:12:49 2020 +0000 @@ -0,0 +1,219 @@ +<?xml version="1.0" ?> +<tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired" + version="2020.8"> + <description>Find and remove adapters in demultiplexed paired-end sequences.</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime cutadapt trim-paired + +--i-demultiplexed-sequences=$idemultiplexedsequences + +--p-cores=$pcores + +#if str($padapterf): + --p-adapter-f=$padapterf +#end if +#if str($pfrontf): + --p-front-f=$pfrontf +#end if +#if '__ob__' in str($panywheref): + #set $panywheref_temp = $panywheref.replace('__ob__', '[') + #set $panywheref = $panywheref_temp +#end if +#if '__cb__' in str($panywheref): + #set $panywheref_temp = $panywheref.replace('__cb__', ']') + #set $panywheref = $panywheref_temp +#end if +#if 'X' in str($panywheref): + #set $panywheref_temp = $panywheref.replace('X', '\\') + #set $panywheref = $panywheref_temp +#end if +#if '__sq__' in str($panywheref): + #set $panywheref_temp = $panywheref.replace('__sq__', "'") + #set $panywheref = $panywheref_temp +#end if +#if '__db__' in str($panywheref): + #set $panywheref_temp = $panywheref.replace('__db__', '"') + #set $panywheref = $panywheref_temp +#end if + +#if str($panywheref): + --p-anywhere-f=$panywheref +#end if + +#if str($padapterr): + --p-adapter-r=$padapterr +#end if +#if str($pfrontr): + --p-front-r=$pfrontr +#end if +#if '__ob__' in str($panywherer): + #set $panywherer_temp = $panywherer.replace('__ob__', '[') + #set $panywherer = $panywherer_temp +#end if +#if '__cb__' in str($panywherer): + #set $panywherer_temp = $panywherer.replace('__cb__', ']') + #set $panywherer = $panywherer_temp +#end if +#if 'X' in str($panywherer): + #set $panywherer_temp = $panywherer.replace('X', '\\') + #set $panywherer = $panywherer_temp +#end if +#if '__sq__' in str($panywherer): + #set $panywherer_temp = $panywherer.replace('__sq__', "'") + #set $panywherer = $panywherer_temp +#end if +#if '__db__' in str($panywherer): + #set $panywherer_temp = $panywherer.replace('__db__', '"') + #set $panywherer = $panywherer_temp +#end if + +#if str($panywherer): + --p-anywhere-r=$panywherer +#end if + +--p-error-rate=$perrorrate + +#if $pnoindels: + --p-no-indels +#end if + +--p-times=$ptimes + +--p-overlap=$poverlap + +#if $pmatchreadwildcards: + --p-match-read-wildcards +#end if + +#if $pnomatchadapterwildcards: + --p-no-match-adapter-wildcards +#end if + +--p-minimum-length=$pminimumlength + +#if $pdiscarduntrimmed: + --p-discard-untrimmed +#end if + +--o-trimmed-sequences=otrimmedsequences + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp otrimmedsequences.qza $otrimmedsequences + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data" /> + <param label="--p-adapter-f: TEXT... Sequence of an adapter ligated to the 3\' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in forward read. If your sequence of interest is \'framed\' by a 5\' and a 3\' adapter, use this parameter to define a \'linked\' primer - see https://cutadapt.readthedocs.io for complete details. [optional]" name="padapterf" optional="False" type="text" value="False" /> + <param label="--p-front-f: TEXT... Sequence of an adapter ligated to the 5\' end. The List[Str] adapter and any preceding bases are trimmed. Partial matches at the 5\' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in forward read. [optional]" name="pfrontf" optional="False" type="text" /> + <param label="--p-anywhere-f: TEXT... Sequence of an adapter that may be ligated to the List[Str] 5\' or 3\' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in forward read. [optional]" name="panywheref" optional="False" type="text" /> + <param label="--p-adapter-r: TEXT... Sequence of an adapter ligated to the 3\' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in reverse read. If your sequence of interest is \'framed\' by a 5\' and a 3\' adapter, use this parameter to define a \'linked\' primer - see https://cutadapt.readthedocs.io for complete details. [optional]" name="padapterr" optional="False" type="text" value="False" /> + <param label="--p-front-r: TEXT... Sequence of an adapter ligated to the 5\' end. The List[Str] adapter and any preceding bases are trimmed. Partial matches at the 5\' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in reverse read. [optional]" name="pfrontr" optional="False" type="text" /> + <param label="--p-anywhere-r: TEXT... Sequence of an adapter that may be ligated to the List[Str] 5\' or 3\' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in reverse read. [optional]" name="panywherer" optional="False" type="text" /> + <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate. [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" /> + <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: True]" name="pnoindels" selected="False" type="boolean" /> + <param label="--p-times: INTEGER Remove multiple occurrences of an adapter if it is Range(1, None) repeated, up to `times` times. [default: 1]" min="1" name="ptimes" optional="True" type="integer" value="1" /> + <param label="--p-overlap: INTEGER Require at least `overlap` bases of overlap between Range(1, None) read and adapter for an adapter to be found. [default: 3]" min="1" name="poverlap" optional="True" type="integer" value="3" /> + <param label="--p-match-read-wildcards: --p-match-read-wildcards: / --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" selected="False" type="boolean" /> + <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pnomatchadapterwildcards" selected="False" type="boolean" /> + <param label="--p-minimum-length: INTEGER Range(1, None) Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" /> + <param label="--p-discard-untrimmed: --p-discard-untrimmed: / --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences" /> + + </outputs> + + <help><![CDATA[ +Find and remove adapters in demultiplexed paired-end sequences. +############################################################### + +Search demultiplexed paired-end sequences for adapters and remove them. The +parameter descriptions in this method are adapted from the official +cutadapt docs - please see those docs at https://cutadapt.readthedocs.io +for complete details. + +Parameters +---------- +demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality] + The paired-end sequences to be trimmed. +cores : Int % Range(1, None), optional + Number of CPU cores to use. +adapter_f : List[Str], optional + Sequence of an adapter ligated to the 3' end. The adapter and any + subsequent bases are trimmed. If a `$` is appended, the adapter is only + found if it is at the end of the read. Search in forward read. If your + sequence of interest is "framed" by a 5' and a 3' adapter, use this + parameter to define a "linked" primer - see + https://cutadapt.readthedocs.io for complete details. +front_f : List[Str], optional + Sequence of an adapter ligated to the 5' end. The adapter and any + preceding bases are trimmed. Partial matches at the 5' end are allowed. + If a `^` character is prepended, the adapter is only found if it is at + the beginning of the read. Search in forward read. +anywhere_f : List[Str], optional + Sequence of an adapter that may be ligated to the 5' or 3' end. Both + types of matches as described under `adapter` and `front` are allowed. + If the first base of the read is part of the match, the behavior is as + with `front`, otherwise as with `adapter`. This option is mostly for + rescuing failed library preparations - do not use if you know which end + your adapter was ligated to. Search in forward read. +adapter_r : List[Str], optional + Sequence of an adapter ligated to the 3' end. The adapter and any + subsequent bases are trimmed. If a `$` is appended, the adapter is only + found if it is at the end of the read. Search in reverse read. If your + sequence of interest is "framed" by a 5' and a 3' adapter, use this + parameter to define a "linked" primer - see + https://cutadapt.readthedocs.io for complete details. +front_r : List[Str], optional + Sequence of an adapter ligated to the 5' end. The adapter and any + preceding bases are trimmed. Partial matches at the 5' end are allowed. + If a `^` character is prepended, the adapter is only found if it is at + the beginning of the read. Search in reverse read. +anywhere_r : List[Str], optional + Sequence of an adapter that may be ligated to the 5' or 3' end. Both + types of matches as described under `adapter` and `front` are allowed. + If the first base of the read is part of the match, the behavior is as + with `front`, otherwise as with `adapter`. This option is mostly for + rescuing failed library preparations - do not use if you know which end + your adapter was ligated to. Search in reverse read. +error_rate : Float % Range(0, 1, inclusive_end=True), optional + Maximum allowed error rate. +indels : Bool, optional + Allow insertions or deletions of bases when matching adapters. +times : Int % Range(1, None), optional + Remove multiple occurrences of an adapter if it is repeated, up to + `times` times. +overlap : Int % Range(1, None), optional + Require at least `overlap` bases of overlap between read and adapter + for an adapter to be found. +match_read_wildcards : Bool, optional + Interpret IUPAC wildcards (e.g., N) in reads. +match_adapter_wildcards : Bool, optional + Interpret IUPAC wildcards (e.g., N) in adapters. +minimum_length : Int % Range(1, None), optional + Discard reads shorter than specified value. Note, the cutadapt default + of 0 has been overridden, because that value produces empty sequence + records. +discard_untrimmed : Bool, optional + Discard reads in which no adapter was found. + +Returns +------- +trimmed_sequences : SampleData[PairedEndSequencesWithQuality] + The resulting trimmed sequences. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file