Mercurial > repos > iuc > mothur_pcr_seqs
diff pcr.seqs.xml @ 0:692381e1abfe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:58:12 -0400 |
| parents | |
| children | 9a1fd25e2a1a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pcr.seqs.xml Fri May 19 05:58:12 2017 -0400 @@ -0,0 +1,159 @@ +<tool profile="16.07" id="mothur_pcr_seqs" name="Pcr.seqs" version="@WRAPPER_VERSION@.0"> + <description>Trim sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + ## create symlinks to input datasets + ln -s "$fasta" fasta.dat && + ln -s "$name_in" name_in.dat && + ln -s "$group_in" group_in.dat && + ln -s "$taxonomy_in" taxonomy_in.dat && + #if $trim.method == "oligos": + ln -s "$trim.oligos" trim.oligos.dat && + #elif $trim.method == "reference": + ln -s "$trim.ecoli" trim.ecoli.dat && + #end if + + echo 'pcr.seqs( + fasta=fasta.dat, + #if $name_in + name=name_in.dat, + #end if + #if $group_in: + group=group_in.dat, + #end if + #if $taxonomy_in: + taxonomy=taxonomy_in.dat, + #end if + #if $trim.method == "oligos": + oligos=trim.oligos.dat, + nomatch=$trim.nomatch, + $trim.keepprimer + #elif $trim.method == "reference": + ecoli=trim.ecoli.dat, + #elif $trim.method == "position": + start=$trim.start, + #if $trim.end and int($trim.end) > 0: + end=$trim.end, + #end if + #end if + #if $pdiffs: + pdiffs=$pdiffs, + #end if + $keepdots + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/> + <conditional name="trim"> + <param name="method" type="select" label="Trim with an oligos file?" help=""> + <option value="oligos">oligos</option> + <option value="reference">reference sequence</option> + <option value="position">start and end positions</option> + </param> + <when value="oligos"> + <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words "forward", "reverse", and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file."/> + <param name="nomatch" type="select" label="nomatch - action when no primer is found"> + <option value="reject" selected="true">reject (default)</option> + <option value="keep">keep</option> + </param> + <param name="keepprimer" type="boolean" falsevalue="" truevalue="keepprimer=true," checked="false" label="keepprimer - keep the primer in the output sequence"/> + </when> + <when value="reference"> + <param name="ecoli" type="data" format="mothur.align" optional="true" label="ecoli - An aligned reference sequence for trimming" help="The ecoli parameter is used to provide a fasta file containing a single reference sequence (e.g. for e. coli) this must be aligned. Mothur will trim to the start and end positions of the reference sequence."/> + </when> + <when value="position"> + <param name="start" type="integer" min="0" value="0" optional="true" label="start - a starting position to trim to"/> + <param name="end" type="integer" value="" optional="true" min="0" label="end - a ending position to trim from"/> + </when> + </conditional> + <param name="keepdots" type="boolean" falsevalue="keepdots=false," truevalue="" checked="true" label="keepdots - keep the leading and trailing alignment dots in the output sequences"/> + <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/> + <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/> + <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/> + <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/> + <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/> + <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${tool.name} on ${on_string}: tax.summary"> + <filter>taxonomy_in</filter> + </data> + <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.groups"> + <filter>group_in</filter> + </data> + <data name="name_out" format="mothur.names" from_work_dir="name_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.names"> + <filter>name_in</filter> + </data> + <data name="accnos_out" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"> + <filter>trim['method'] =='oligos'</filter> + </data> + </outputs> + <tests> + <test><!-- test with position method --> + <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> + <param name="keepdots" value=""/> + <param name="method" value="position"/> + <param name="start" value="0"/> + <param name="end" value="0"/> + <param name="pdiffs" value="0"/> + <expand macro="logfile-test"/> + <output name="pcr_fasta" md5="4f9c3a835bbba51c64fbf86c8a467d0e" ftype="mothur.align"/> + <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> + </test> + <test><!-- test with reference method --> + <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> + <param name="keepdots" value="keepdots=false,"/> + <param name="method" value="reference"/> + <param name="ecoli" value="amazon.align_head"/> + <param name="name_in" value="amazon.align_head.names"/> + <param name="pdiffs" value="2"/> + <expand macro="logfile-test"/> + <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/> + <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> + <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/> + </test> + <test><!-- test with oligos and all outputs --> + <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> + <param name="method" value="oligos"/> + <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/> + <param name="name_in" value="amazon.names" ftype="mothur.names"/> + <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> + <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> + <param name="start" value="5"/> + <param name="end" value="50"/> + <expand macro="logfile-test"/> + <output name="pcr_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> + <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/> + <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/> + <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/> + <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/> + <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The pcr.seqs_ command assigns sequences to chosen taxonomy outline. + +.. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs + +]]> + </help> + <expand macro="citations"/> +</tool>