Mercurial > repos > iuc > mothur_filter_seqs
diff filter.seqs.xml @ 0:870f2a438139 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:26:45 -0400 |
parents | |
children | c799faca02a1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.seqs.xml Fri May 19 05:26:45 2017 -0400 @@ -0,0 +1,102 @@ +<tool profile="16.07" id="mothur_filter_seqs" name="Filter.seqs" version="@WRAPPER_VERSION@.0"> + <description>removes columns from alignments</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 && + #for $i in $inputs: + ln -s "$i.fasta" fasta${inputs.index($i)}.dat && + #end for + ln -s "$hard" hard.dat && + + echo 'filter.seqs( + fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#, + vertical=$vertical, + #if $trump: + trump=$trump, + #end if + soft=$soft, + #if $hard: + hard=hard.dat, + #end if + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log && + + ## rename collection files for more transparent element naming + mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta + #for i in $inputs: + && mv fasta${inputs.index($i)}.filter.fasta "${i.fasta.element_identifier}".filter.fasta + #end for + ]]></command> + <inputs> + <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> + <repeat name="inputs" title="Additional Alignment File"> + <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> + </repeat> + <param name="vertical" type="boolean" checked="true" truevalue="true" falsevalue="false" label="vertical - Vertical column" help="Ignore any column that only contains gap characters (i.e. '-' or '.')"/> + <param name="trump" type="select" label="trump - Trump character" help="Remove a column if the trump character is found at that position in any sequence of the alignment"> + <option value="">Off</option> + <option value=".">.</option> + <option value="-">-</option> + <option value="N">N</option> + </param> + <param name="soft" type="integer" value="0" min="0" max="100" label="soft - percentage required to retain column. (0-100)" help="Removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences"/> + <param name="hard" type="data" format="mothur.filter" optional="True" label="hard - Hard Column Filter" help="A file should only contain one line consisting of 0's and 1's"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="out_filter" format="mothur.filter" from_work_dir="fasta*.filter" label="${tool.name} on ${on_string}: filter"/> + <collection name="filteredfastas" type="list" label="${tool.name} on ${on_string}: filtered fastas"> + <discover_datasets pattern="(?P<designation>.*)\.filter\.fasta" format="fasta"/> + <filter>inputs</filter> <!-- only output collection if multiple outputs--> + </collection> + <data name="filteredfasta" format="fasta" from_work_dir="*.filter.fasta" label="${tool.name} on ${on_string}: filtered fasta"> + <filter>not inputs</filter> + </data> + </outputs> + <tests> + <test><!-- test with multiple inputs and collection output --> + <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> + <repeat name="inputs"> + <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/> + </repeat> + <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/> + <output_collection name="filteredfastas" count="2"> + <element name="HMP_MOCK.v35.align" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc" ftype="fasta"/> + </output_collection> + <expand macro="logfile-test"/> + </test> + <test><!-- test with single input and non-collection output --> + <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> + <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/> + <output name="filteredfasta" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them. By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs. + +.. _filter.seqs: https://www.mothur.org/wiki/Filter.seqs + +v.1.20.0: Updated to Mothur 1.33 + +]]> + </help> + <expand macro="citations"/> +</tool>