Mercurial > repos > iuc > mothur_pcr_seqs
diff pcr.seqs.xml @ 2:9a1fd25e2a1a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:19:52 -0400 |
parents | 692381e1abfe |
children |
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--- a/pcr.seqs.xml Tue Sep 05 17:06:09 2017 -0400 +++ b/pcr.seqs.xml Tue Mar 20 22:19:52 2018 -0400 @@ -7,54 +7,53 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@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 +## 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 +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=$trim.end, + #end if + #end if + pdiffs=$pdiffs, + rdiffs=$rdiffs, + $keepdots + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> - <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/> + <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Sequences" help="sequences must be aligned"/> <conditional name="trim"> <param name="method" type="select" label="Trim with an oligos file?" help=""> <option value="oligos">oligos</option> @@ -81,12 +80,14 @@ <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/> <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/> <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/> - <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/> + <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the forward primers (default 0)"/> + <param name="rdiffs" type="integer" value="0" min="0" label="rdiffs - number of differences to allow in the reverse primers (default 0)"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> - <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta.pcr.dat" label="${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 ${on_string}: pcr.scrap.fasta"/> + <data name="pcr_fasta" format_source="fasta" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/> + <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap.pcr.dat" label="${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> @@ -108,6 +109,7 @@ <param name="start" value="0"/> <param name="end" value="0"/> <param name="pdiffs" value="0"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> <output name="pcr_fasta" md5="4f9c3a835bbba51c64fbf86c8a467d0e" ftype="mothur.align"/> <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> @@ -116,9 +118,10 @@ <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="ecoli" value="amazon.align_head" ftype="mothur.align"/> <param name="name_in" value="amazon.align_head.names"/> <param name="pdiffs" value="2"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/> <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> @@ -133,6 +136,7 @@ <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> <param name="start" value="5"/> <param name="end" value="50"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> <output name="pcr_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/> @@ -142,8 +146,7 @@ <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -153,7 +156,6 @@ .. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>