Mercurial > repos > iuc > mothur_screen_seqs
diff screen.seqs.xml @ 0:125a6ae65887 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 05:48:41 -0400 |
parents | |
children | 8743aecd26a9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/screen.seqs.xml Fri May 19 05:48:41 2017 -0400 @@ -0,0 +1,162 @@ +<tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.0"> + <description>Screen sequences</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 "$fasta_in" fasta_in.dat && + ln -s "$names_in" names_in.dat && + ln -s "$groups_in" groups_in.dat && + ln -s "$qfile_in" qfile_in.dat && + ln -s "$count_in" count_in.dat && + ln -s "$alignreport_in" alignreport_in.dat && + ln -s "$taxonomy_in" taxonomy_in.dat && + ln -s "$summary" summary.dat && + ln -s "$contigsreport" contigsreport.dat && + + echo 'screen.seqs( + fasta=fasta_in.dat + #if int($start) > -1: + ,start=$start + #end if + #if int($end) > -1: + ,end=$end + #end if + #if int($minlength) > -1: + ,minlength=$minlength + #end if + #if int($maxlength) > -1: + ,maxlength=$maxlength + #end if + #if int($maxambig) > -1: + ,maxambig=$maxambig + #end if + #if int($maxhomop) > -1: + ,maxhomop=$maxhomop + #end if + #if int($criteria) > -1: + ,criteria=$criteria + #end if + #if $optimize: + ,optimize=$optimize + #end if + #if $qfile_in: + ,qfile=qfile_in.dat + #end if + #if $names_in: + ,name=names_in.dat + #end if + #if $groups_in: + ,group=groups_in.dat + #end if + #if $alignreport_in: + ,alignreport=alignreport_in.dat + #end if + #if $taxonomy_in: + ,taxonomy=taxonomy_in.dat + #end if + #if $count_in: + ,count=count_in.dat + #end if + #if $summary: + ,summary=summary.dat + #end if + #if $contigsreport: + ,contigsreport=contigsreport.dat + #end if + ,processors='"\${GALAXY_SLOTS:-8}"' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/> + <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/> + <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/> + <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/> + <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/> + <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/> + <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/> + <param name="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained(ignored when negative)"/> + <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters"> + <option value="start">start</option> + <option value="end">end</option> + <option value="minlength">minlength</option> + <option value="maxlength">maxlength</option> + <option value="maxambig">maxambig</option> + <option value="maxhomop">maxhomop</option> + </param> + <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/> + <param name="names_in" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/> + <param name="groups_in" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/> + <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report to screen"/> + <param name="summary" type="data" format="mothur.summary" optional="true" label="summary file - as created by summary.seqs" help="saves processing time when screening with parameters in the summary file"/> + <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - Contigs Report to screen with" help="this file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/> + <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> + <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.good.dat" label="${tool.name} on ${on_string}: good.${fasta_in.datatype.file_ext}"/> + <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta_in*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/> + <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.good.dat" label="${tool.name} on ${on_string}: qfile"> + <filter>qfile_in</filter> + </data> + <data name="names_out" format="mothur.names" from_work_dir="names_in*.good.dat" label="${tool.name} on ${on_string}: names"> + <filter>names_in</filter> + </data> + <data name="groups_out" format="mothur.groups" from_work_dir="groups_in*.good.dat" label="${tool.name} on ${on_string}: groups"> + <filter>groups_in</filter> + </data> + <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.good.dat" label="${tool.name} on ${on_string}: align.report"> + <filter>alignreport_in</filter> + </data> + <data name="count_out" format="mothur.count_table" from_work_dir="count_in*.good.dat" label="${tool.name} on ${on_string}: count"> + <filter>count_in</filter> + </data> + </outputs> + <tests> + <test> + <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> + <param name="maxambig" value="0"/> + <param name="maxlength" value="275"/> + <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/> + <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/> + <expand macro="logfile-test"/> + </test> + <test> + <param name="fasta_in" value="amazon.fasta" ftype="mothur.align"/> + <param name="count_in" value="amazon.count_table"/> + <param name="maxambig" value="0"/> + <param name="maxlength" value="275"/> + <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> + <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee" ftype="mothur.count_table"/> + <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5" ftype="mothur.accnos"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file. + +.. _name: https://www.mothur.org/wiki/Name_file +.. _group: https://www.mothur.org/wiki/Group_file +.. _align.report: https://www.mothur.org/wiki/Align.seqs +.. _screen.seqs: https://www.mothur.org/wiki/Screen.seqs + +]]> + </help> + <expand macro="citations"/> +</tool>