Mercurial > repos > iuc > mothur_get_sharedseqs
diff get.sharedseqs.xml @ 0:1d496917a707 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:21:47 -0400 |
| parents | |
| children | d5b97213e4ba |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get.sharedseqs.xml Fri May 19 05:21:47 2017 -0400 @@ -0,0 +1,213 @@ +<tool profile="16.07" id="mothur_get_sharedseqs" name="Get.sharedseqs" version="@WRAPPER_VERSION@.0"> + <description>Get shared sequences at each distance from list and group</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 "$infile.otu" infile_otu.dat && + #if $infile.intype == "in_listgroup": + ln -s "$infile.group" infile.group.dat && + ln -s "$infile.fasta" infile_fasta.dat && + #end if + + echo 'get.sharedseqs( + #if $infile.intype == "in_listgroup": + list=infile_otu.dat + ,group=infile.group.dat + #if $infile.fasta: + ,fasta=infile_fasta.dat + #end if + #else + shared=infile_otu.dat + #end if + #if $infile.label: + ,label=${ str($infile.label).replace(",","-") } + #end if + #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups: + ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") } + #end if + #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups: + ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") } + #end if + #if $output: + ,output=$output + #end if + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <conditional name="infile"> + <param name="intype" type="select" label="Will you be supplying a shared file or a list and group file?" help=""> + <option value="in_shared">Shared file</option> + <option value="in_listgroup">OTU list and group file</option> + </param> + <when value="in_shared"> + <param name="otu" type="data" format="mothur.shared" label="list - OTU List or shared file"/> + <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> + <options> + <filter type="data_meta" ref="otu" key="labels"/> + </options> + </param> + <conditional name="seqsfrom"> + <param name="selection" type="select" label="Select Groups" help=""> + <option value="all" selected="true">None (use all groups)</option> + <option value="unique">OTUs that contain ONLY sequences from the selected groups</option> + <option value="shared">OTUs that contain sequences from the selected groups</option> + </param> + <when value="unique"> + <param name="groups" type="select" multiple="true" label="unique - Group to analyze"> + <options> + <filter type="data_meta" ref="otu" key="groups"/> + </options> + </param> + </when> + <when value="shared"> + <param name="groups" type="select" multiple="true" label="shared - Groups to analyze"> + <options> + <filter type="data_meta" ref="otu" key="groups"/> + </options> + </param> + </when> + <when value="all"/> + </conditional> + </when> + <when value="in_listgroup"> + <param name="otu" type="data" format="mothur.list" label="list - OTU List or shared file"/> + <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels to include" help="By default all are included if no selection is made"> + <options> + <filter type="data_meta" ref="otu" key="labels"/> + </options> + </param> + <param name="group" type="data" format="mothur.groups" optional="true" label="group - not required if using a shared file"/> + <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset" help="will output a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified"/> + <conditional name="seqsfrom"> + <param name="selection" type="select" label="Select Groups" help=""> + <option value="all" selected="true">None (use all groups)</option> + <option value="unique">OTUs that contain ONLY sequences from the selected groups</option> + <option value="shared">OTUs that contain sequences from the selected groups</option> + </param> + <when value="unique"> + <param name="groups" type="select" multiple="true" label="unique - Group to analyze"> + <options> + <filter type="data_meta" ref="group" key="groups"/> + </options> + </param> + </when> + <when value="shared"> + <param name="groups" type="select" multiple="true" label="shared - Groups to analyze"> + <options> + <filter type="data_meta" ref="group" key="groups"/> + </options> + </param> + </when> + <when value="all"/> + </conditional> + </when> + </conditional> + <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs"> + <option value="" selected="true">default: (name group bin_number)</option> + <option value="accnos">accnos (name)</option> + </param> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <collection name="sharedseqs" type="list" label="${tool.name} on ${on_string}: shared.seqs"> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.shared\.seqs" format="tabular"/> + <filter>output != 'accnos'</filter> + </collection> + <collection name="sharedaccnos" type="list" label="${tool.name} on ${on_string}: shared.accnos"> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.accnos" format="mothur.accnos"/> + <filter>output == 'accnos'</filter> + </collection> + <collection name="sharedfastas" type="list" label="${tool.name} on ${on_string}: shared.fastas"> + <discover_datasets pattern=".*?\.(?P<designation>.*)\.shared\.fasta" format="fasta"/> + <filter>infile['fasta']</filter> + </collection> + </outputs> + <tests> + <test><!-- test with shared file --> + <param name="intype" value="in_shared"/> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="selection" value="shared"/> + <output_collection name="sharedseqs" count="35"> + <element name="0.41.unique.forest-pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with list and group file --> + <param name="intype" value="in_listgroup"/> + <param name="otu" value="amazon.an.list" ftype="mothur.list"/> + <param name="group" value="amazon.groups" ftype="mothur.groups"/> + <output_collection name="sharedseqs" count="35"> + <element name="0.41.unique.forest-pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with shared seqs and subset of labels --> + <param name="intype" value="in_shared"/> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="selection" value="shared"/> + <param name="groups" value="forest,pasture"/> + <param name="label" value="0.03,0.33,0.41"/> + <output_collection name="sharedseqs" count="3"> + <element name="0.41.forest-pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with unique seqs and subset of groups --> + <param name="intype" value="in_shared"/> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="selection" value="unique"/> + <param name="groups" value="pasture"/> + <output_collection name="sharedseqs" count="34"> + <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with accnos output --> + <param name="intype" value="in_shared"/> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="output" value="accnos"/> + <output_collection name="sharedaccnos" count="35"> + <element name="0.41.unique.forest-pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with fasta input and output --> + <param name="intype" value="in_listgroup"/> + <param name="otu" value="amazon.an.list" ftype="mothur.list"/> + <param name="group" value="amazon.groups" ftype="mothur.groups"/> + <param name="fasta" value="amazon.fasta" ftype="fasta"/> + <output_collection name="sharedseqs" count="35"> + <element name="0.41.unique.forest-pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/> + </output_collection> + <output_collection name="sharedfastas" count="35"> + <element name="0.41.unique.forest-pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The get.sharedseqs_ command takes a list and group file and outputs a .shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify. + +.. _get.sharedseqs: https://www.mothur.org/wiki/Get.sharedseqs + +v1.21.0: Updated to Mothur 1.33, added shared file option +]]> + </help> + <expand macro="citations"/> +</tool>