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view sub.sample.xml @ 5:2986f7b01e74 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 68e35d5f24a9219e5583ede7d38a78fa976f7dbb
author | iuc |
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date | Sat, 14 Jul 2018 23:11:05 -0400 |
parents | 46d13e8c60ba |
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<tool profile="16.07" id="mothur_sub_sample" name="Sub.sample" version="@WRAPPER_VERSION@.0"> <description>Create a sub sample</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 '$input.otu' input_otu.dat && ln -s '$count' count.dat && ln -s '$taxonomy' taxonomy.dat && #if $input.format == "fasta": ln -s '$input.name_in' input_name_in.dat && #end if #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes": ln -s '$input.use_group.group_in' input_use_group_group_in.dat && #end if echo 'sub.sample( #if $input.format == "fasta": fasta=input_otu.dat #if $input.name_in: ,name=input_name_in.dat #end if #else #if $input.format == "list": list=input_otu.dat #elif $input.format == "sabund": sabund=input_otu.dat #elif $input.format == "rabund": rabund=input_otu.dat #elif $input.format == "shared": shared=input_otu.dat #if $input.groups: ,groups=${ str($input.groups).replace(",","-") } #end if #end if #if $input.label: ,label=${ str($input.label).replace(",","-") } #end if #end if #if $input.format == "fasta" or $input.format == "list": #if $input.use_group.to_filter == "yes": ,group=input_use_group_group_in.dat #if $input.use_group.groups: ,groups=${ str($input.use_group.groups).replace(",","-") } #end if ,persample=$input.use_group.persample #end if #end if #if $count: ,count=count.dat #end if #if $taxonomy: ,taxonomy=taxonomy.dat #end if #if $size: ,size=$size #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <conditional name="input"> <param name="format" type="select" label="Select type of data to sub sample"> <option value="fasta">FASTA</option> <option value="list">OTU List</option> <option value="shared">OTU Shared</option> <option value="sabund">OTU Shared Abundance (sabund)</option> <option value="rabund">OTU Relative Abundance (rabund)</option> </param> <when value="fasta"> <param name="otu" type="data" format="fasta" label="fasta - "/> <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Group Names from your history"/> <conditional name="use_group"> <param name="to_filter" type="select" label="Use groups?"> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> <options> <filter type="data_meta" ref="group_in" key="groups"/> </options> </param> <param name="persample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="persample - select subsample of the same size from each of the groups"/> </when> </conditional> </when> <when value="list"> <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> <conditional name="use_group"> <param name="to_filter" type="select" label="Use groups"> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> <options> <filter type="data_meta" ref="group_in" key="groups"/> </options> </param> <param name="persample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="persample - select subsample of the same size from each of the groups"/> </when> </conditional> <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> <expand macro="labeloptions"/> </param> </when> <when value="shared"> <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> <options> <filter type="data_meta" ref="otu" key="groups"/> </options> </param> <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> <expand macro="labeloptions"/> </param> </when> <when value="sabund"> <param name="otu" type="data" format="mothur.sabund" label="sabund - OTU Species Abundance"/> <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> <expand macro="labeloptions"/> </param> </when> <when value="rabund"> <param name="otu" type="data" format="mothur.rabund" label="rabund - OTU Relative Abundance"/> <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> <expand macro="labeloptions"/> </param> </when> </conditional> <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/> <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta"> <filter>input['format'] == 'fasta'</filter> </data> <data name="taxonomy_out" format_source="taxonomy" from_work_dir="taxonomy.subsample.dat" label="${tool.name} on ${on_string}: subsample.taxonomy"> <filter>taxonomy</filter> </data> <collection name="list_out" type="list" label="${tool.name} on ${on_string}: subsample.list"> <filter>input['format'] == 'list'</filter> <discover_datasets pattern=".*?\.(?P<designation>.*)\.subsample\.dat" format="mothur.list"/> </collection> <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: subsample.shared"> <filter>input['format'] == 'shared'</filter> <discover_datasets pattern=".*?\.(?P<designation>.*)\.subsample\.dat" format="mothur.shared"/> </collection> <data name="sabund_out" format="mothur.sabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.sabund"> <filter>input['format'] == 'sabund'</filter> </data> <data name="rabund_out" format="mothur.rabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.rabund"> <filter>input['format'] == 'rabund'</filter> </data> <data name="names_out" format="mothur.names" from_work_dir="input_name_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.names"> <filter>input['format'] == 'fasta' and input['name_in']</filter> </data> <data name="group_out" format="mothur.groups" from_work_dir="input_use_group_group_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.groups"> <filter>(input['format'] == 'fasta' or input['format'] == 'list') and input['use_group']['to_filter'] == 'yes'</filter> </data> <data name="count_out" format="mothur.count_table" from_work_dir="count.subsample.*" label="${tool.name} on ${on_string}: subsample.count"> <filter>count</filter> </data> </outputs> <tests> <test><!-- test with list --> <param name="format" value="list"/> <param name="otu" value="amazon.an.list" ftype="mothur.list"/> <output_collection name="list_out" count="36"> <element name="0.20" ftype="mothur.list"> <assert_contents> <has_text text="label"/> <has_text text="numOtus"/> </assert_contents> </element> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with list and group file and label select--> <param name="format" value="list"/> <param name="otu" value="amazon.an.list" ftype="mothur.list"/> <param name="to_filter" value="yes"/> <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> <param name="groups" value="forest,pasture"/> <param name="label" value="0.20,0.45,0.55"/> <output_collection name="list_out" count="3"> <element name="0.20" ftype="mothur.list"> <assert_contents> <has_text text="label"/> <has_text text="numOtus"/> </assert_contents> </element> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with fasta and taxonomy --> <param name="format" value="fasta"/> <param name="otu" value="amazon.fasta" ftype="fasta"/> <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> <output name="fasta_out" ftype="fasta"> <assert_contents> <has_text text=">U"/> </assert_contents> </output> <output name="taxonomy_out" ftype="mothur.seq.taxonomy"> <assert_contents> <has_line_matching expression="^U[0-9]+\tBacteria.*$"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with fasta and group file and name file --> <param name="format" value="fasta"/> <param name="otu" value="amazon.fasta" ftype="fasta"/> <param name="to_filter" value="yes"/> <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> <param name="groups" value="forest,pasture"/> <param name="name_in" value="amazon1.names" ftype="mothur.names"/> <output name="fasta_out" ftype="fasta"> <assert_contents> <has_text_matching expression=">U[0-9]+"/> </assert_contents> </output> <output name="group_out" ftype="mothur.groups"> <assert_contents> <has_line_matching expression="^U[0-9]+\t(forest|pasture)$"/> </assert_contents> </output> <output name="names_out" ftype="mothur.names"> <assert_contents> <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with shared --> <param name="format" value="shared"/> <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <param name="label" value="unique,0.20"/> <param name="groups" value="forest"/> <output_collection name="shared_out" count="2"> <element name="0.20" ftype="mothur.shared"> <assert_contents> <has_text text="label"/> <has_text text="numOtus"/> <has_text text="forest"/> <not_has_text text="pasture"/> </assert_contents> </element> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with rabund --> <param name="format" value="rabund"/> <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/> <output name="rabund_out" ftype="mothur.rabund"> <assert_contents> <has_text text="unique"/> <has_text text="0.55"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with sabund --> <param name="format" value="sabund"/> <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> <output name="sabund_out" ftype="mothur.sabund"> <assert_contents> <has_text text="unique"/> <has_text text="0.55"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with count file --> <param name="format" value="fasta"/> <param name="otu" value="amazon.unique.fasta" ftype="fasta"/> <param name="count" value="amazon.count_table" ftype="mothur.count_table"/> <output name="count_out" ftype="mothur.count_table"> <assert_contents> <expand macro="test-count-format"/> <has_line_matching expression="^U\d+\t\d$"/> </assert_contents> </output> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The sub.sample_ command can be used as a way to normalize your data, or to create a smaller set from your original set. It takes as an input the following file types: fasta, list_, shared_, rabund_ and sabund_ to generate a new file that contains a sampling of your original file. .. _list: https://www.mothur.org/wiki/List_file .. _shared: https://www.mothur.org/wiki/Shared_file .. _rabund: https://www.mothur.org/wiki/Rabund_file .. _sabund: https://www.mothur.org/wiki/Sabund_file .. _sub.sample: https://www.mothur.org/wiki/Sub.sample ]]></help> <expand macro="citations"/> </tool>