Mercurial > repos > iuc > mothur_remove_lineage
diff remove.lineage.xml @ 0:5a18d3d09b80 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:25:21 -0400 |
| parents | |
| children | d46157fb52cd |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/remove.lineage.xml Fri May 19 05:25:21 2017 -0400 @@ -0,0 +1,212 @@ +<tool profile="16.07" id="mothur_remove_lineage" name="Remove.lineage" version="@WRAPPER_VERSION@.0"> + <description>Picks by taxon</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + #import re + ## create symlinks to input datasets + ln -s "$file.taxonomy" file.taxonomy.dat && + #if $file.filetype == "useconstaxonomy": + ln -s "$file.shared" file.shared.dat && + ln -s "$file.list" file.list.dat && + #end if + ln -s "$fasta_in" fasta_in.dat && + ln -s "$group_in" group_in.dat && + ln -s "$alignreport_in" alignreport_in.dat && + ln -s "$list_in" list_in.dat && + ln -s "$name_in" name_in.dat && + ln -s "$count" count.dat && + + echo 'remove.lineage( + #if $file.filetype == "usetaxonomy": + taxonomy=file.taxonomy.dat + #else + constaxonomy=file.taxonomy.dat + #if $file.shared: + ,shared=file.shared.dat + #end if + #if $file.list: + ,list=file.list.dat + #end if + #end if + #if $file.taxons: + #set taxonstring=str($file.taxons).replace(",","-") + ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"' + #elif $taxon: + ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"' + #end if + #if $fasta_in: + ,fasta=fasta_in.dat + #end if + #if $group_in: + ,group=group_in.dat + #end if + #if $alignreport_in: + ,alignreport=alignreport_in.dat + #end if + #if $list_in: + ,list=list_in.dat + #end if + #if $name_in: + ,name=name_in.dat + ,dups=$dups + #end if + #if $count: + ,count=count.dat + #end if + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <conditional name="file"> + <param name="filetype" type="select" label="choose which file is used"> + <option value="usetaxonomy" selected="true">taxonomy</option> + <option value="useconstaxonomy">constaxonomy</option> + </param> + <when value="usetaxonomy"> + <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy" help="please make sure your file has no quotation marks in it"/> + <param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy"> + <options from_dataset="taxonomy"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="unique_value" name="unique_taxon" column="1"/> + <filter type="sort_by" name="sorted_taxon" column="1"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value=";"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + </when> + <when value="useconstaxonomy"> + <param name="taxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file" help="please make sure your file has no quotation marks in it"/> + <param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy"> + <options from_dataset="taxonomy"> + <column name="name" index="2"/> + <column name="value" index="2"/> + <filter type="unique_value" name="unique_taxon" column="2"/> + <filter type="sort_by" name="sorted_taxon" column="2"/> + </options> + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <add value=";"/> + <remove value="""/> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param name="shared" type="data" format="mothur.shared" label="shared - shared file" optional="true"/> + <param name="list" type="data" format="mothur.list" label="list - list file" optional="true"/> + </when> + </conditional> + <param name="taxon" type="text" area="True" size="5x120" label="taxon - Manually select Taxons for filtering" help="If no taxons selected from file, Enter 1 or more taxons separated by dashes here, e.g. Bacteria;Firmicutes;-Bacteria;Actinobacteria; "/> + <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> + <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Groups"/> + <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> + <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> + <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> + <param name="dups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="dups - Apply to duplicate names"/> + <param name="count" type="data" format="mothur.count_table" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="file.taxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy"/> + <data format_source="fasta_in" name="fasta_out" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> + <filter>fasta_in</filter> + </data> + <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.group"> + <filter>group_in</filter> + </data> + <data name="count_out" format="mothur.count_table" from_work_dir="count*.pick.*" label="${tool.name} on ${on_string}: pick.count_table"> + <filter>count</filter> + </data> + <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list"> + <filter>list_in</filter> + <discover_datasets pattern="list_in.*?\.(?P<designation>.*)\.pick.*" format="mothur.list"/> + </collection> + <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name"> + <filter>name_in</filter> + </data> + <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.pick.*" label="${tool.name} on ${on_string}: pick.align.report"> + <filter>alignreport_in</filter> + </data> + </outputs> + <tests> + <test><!-- test with defaults and single taxon --> + <param name="filetype" value="usetaxonomy"/> + <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> + <param name="taxon" value="Bacteria;Firmicutes;"/> + <param name="count" value="amazon.count_table"/> + <output name="taxonomy_out" md5="a2a72b7f53ef6c907b8c4db906fcf03e"/> + <output name="count_out" md5="6f89b3b99f337414d98f70fcda4b248e"/> + </test> + <test><!-- test with multiple taxons and all additional files --> + <param name="filetype" value="usetaxonomy"/> + <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> + <param name="taxon" value="Bacteria;Firmicutes;,Bacteria;Actinobacteria;"/> + <param name="group_in" value="abrecovery.groups" ftype="mothur.groups"/> + <param name="fasta_in" value="abrecovery.fasta" ftype="fasta"/> + <param name="name_in" value="abrecovery.names" ftype="mothur.names"/> + <param name="alignreport_in" value="Mock_S280_L001_R1_001_small.contigs.report" ftype="mothur.align.report"/> + <param name="list_in" value="amazon.an.list" ftype="mothur.list"/> + <output name="taxonomy_out" md5="449200280fa6c332854204fe78a9bd12"/> + <output name="group_out" md5="119a2642bd730aad03f7d6c1f8b57a0b" ftype="mothur.groups"/> + <output name="fasta_out" md5="2c8415a797011e15f19ad85a9c994551" ftype="fasta"/> + <output name="name_out" md5="712b28c3a84d3c16ef202340717e3a91" ftype="mothur.names"/> + <output name="alignreport_out" md5="d94be921c3ad1786db3e60dc23c3bc04" ftype="mothur.align.report"/> + <output_collection name="list_out" count="36"> + <element name="0.05" md5="5d4195793e2fc50979b377df468c436a" ftype="mothur.list"/> + </output_collection> + </test> + <test><!-- test with taxons from file --> + <param name="filetype" value="usetaxonomy"/> + <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> + <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);,Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);"/> + <output name="taxonomy_out" md5="57b4ab4e5b68f8c7d88a0f591c4fe4a1"/> + </test> + <test><!-- test with constaxonomy file --> + <param name="filetype" value="useconstaxonomy"/> + <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/> + <param name="taxon" value="Bacteria;Bacteroidetes;"/> + <output name="taxonomy_out" md5="751fd9b99828998dd909115634027e5e"/> + </test> + <test><!-- test with constaxonomy file and taxons from file --> + <param name="filetype" value="useconstaxonomy"/> + <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/> + <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;,Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"/> + <output name="taxonomy_out" md5="017f53dd82f3e1afcf48778034b51685"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The remove.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences. + +.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline +.. _name: https://www.mothur.org/wiki/Name_file +.. _group: https://www.mothur.org/wiki/Group_file +.. _list: https://www.mothur.org/wiki/List_file +.. _align.report: https://www.mothur.org/wiki/Align.seqs +.. _remove.lineage: https://www.mothur.org/wiki/Remove.lineage + +]]> + </help> + <expand macro="citations"/> +</tool>