Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_cutadapt_trim-paired.xml @ 14:a0a8d77a991c draft
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| author | florianbegusch |
|---|---|
| date | Thu, 03 Sep 2020 09:51:29 +0000 |
| parents | f190567fe3f6 |
| children |
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--- a/qiime2/qiime_cutadapt_trim-paired.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_cutadapt_trim-paired.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,116 +1,88 @@ <?xml version="1.0" ?> -<tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired" version="2019.7"> - <description> - Find and remove adapters in demultiplexed paired-end sequences.</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<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 -#set $pcores = '${GALAXY_SLOTS:-4}' -#if str($pcores): --p-cores=$pcores -#end if - - - -#if '__sq__' in str($padapterf): - #set $padapterf_temp = $padapterf.replace('__sq__', "'") - #set $padapterf = $padapterf_temp -#end if - -#if 'X' in str($padapterf): - #set $padapterf_temp = $padapterf.replace('X', "$") - #set $padapterf = $padapterf_temp -#end if #if str($padapterf): - --p-adapter-f="$padapterf" + --p-adapter-f=$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 = $panywheref_temp #end if - - - - -#if '__sq__' in str($pfrontf): - #set $pfrontf_temp = $pfrontf.replace('__sq__', "'") - #set $pfrontf = $pfrontf_temp +#if '__cb__' in str($panywheref): + #set $panywheref_temp = $panywheref.replace('__cb__', ']') + #set $panywheref = $panywheref_temp #end if - -#if str($pfrontf): - --p-front-f="$pfrontf" +#if 'X' in str($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 = $panywheref_temp #end if - -#if str($panywheref): - --p-anywhere-f="$panywheref" +#if '__db__' in str($panywheref): + #set $panywheref_temp = $panywheref.replace('__db__', '"') + #set $panywheref = $panywheref_temp #end if - - - - -#if '__sq__' in str($padapterr): - #set $padapterr_temp = $padapterr.replace('__sq__', "'") - #set $padapterr = $padapterr_temp -#end if - -#if 'X' in str($padapterr): - #set $padapterr_temp = $padapterr.replace('X', "$") - #set $padapterr = $padapterr_temp +#if str($panywheref): + --p-anywhere-f=$panywheref #end if #if str($padapterr): - --p-adapter-r="$padapterr" + --p-adapter-r=$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 = $panywherer_temp #end if - - - -#if '__sq__' in str($pfrontr): - #set $pfrontr_temp = $pfrontr.replace('__sq__', "'") - #set $pfrontr = $pfrontr_temp +#if '__cb__' in str($panywherer): + #set $panywherer_temp = $panywherer.replace('__cb__', ']') + #set $panywherer = $panywherer_temp #end if - -#if str($pfrontr): - --p-front-r="$pfrontr" +#if 'X' in str($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 = $panywherer_temp #end if - -#if str($panywherer): - --p-anywhere-r="$panywherer" +#if '__db__' in str($panywherer): + #set $panywherer_temp = $panywherer.replace('__db__', '"') + #set $panywherer = $panywherer_temp #end if - +#if str($panywherer): + --p-anywhere-r=$panywherer +#end if -#if str($perrorrate): - --p-error-rate=$perrorrate -#end if +--p-error-rate=$perrorrate #if $pnoindels: --p-no-indels #end if -#if $ptimes: - --p-times=$ptimes -#end if +--p-times=$ptimes -#if str($poverlap): - --p-overlap=$poverlap -#end if +--p-overlap=$poverlap #if $pmatchreadwildcards: --p-match-read-wildcards @@ -120,40 +92,48 @@ --p-no-match-adapter-wildcards #end if -#if $pminimumlength: - --p-minimum-length=$pminimumlength -#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="True" type="text"/> - <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="True" 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="True" 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="True" type="text"/> - <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="True" 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="True" type="text"/> - <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/> - <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: False]" 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]" name="ptimes" optional="True" type="integer" min="1" 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]" name="poverlap" optional="True" type="integer" min="1" value="3"/> - <param label="--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: False]" 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]" name="pminimumlength" optional="True" type="integer" min="1" value="1"/> - <param label="--p-discard-untrimmed: --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean"/> - </inputs> - <outputs> - <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences"/> - </outputs> - <help><![CDATA[ + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data" /> + <param label="--p-adapter-f: TEXT... Sequence of an adapter ligated to the 3\' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` 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 ${on_string}: trimmedsequences.qza" name="otrimmedsequences" /> + + </outputs> + + <help><![CDATA[ Find and remove adapters in demultiplexed paired-end sequences. ############################################################### @@ -166,6 +146,8 @@ ---------- demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. +cores : Int % Range(1, None), optional + Number of CPU cores to use. adapter_f : List[Str], optional Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only @@ -229,9 +211,9 @@ ------- trimmed_sequences : SampleData[PairedEndSequencesWithQuality] The resulting trimmed sequences. - ]]></help> -<macros> + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file