Mercurial > repos > sanbi-uwc > mothur_test
diff tools/mothur/screen.seqs.xml @ 0:ee4fee239fe7 draft default tip
planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author | sanbi-uwc |
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date | Fri, 03 Jun 2016 09:32:47 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mothur/screen.seqs.xml Fri Jun 03 09:32:47 2016 -0400 @@ -0,0 +1,171 @@ +<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="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + echo 'screen.seqs( + fasta=$fasta_in + #if $start > -1: + ,start=$start + #end if + #if $end > -1: + ,end=$end + #end if + #if $minlength > -1: + ,minlength=$minlength + #end if + #if $maxlength > -1: + ,maxlength=$maxlength + #end if + #if $maxambig > -1: + ,maxambig=$maxambig + #end if + #if $maxhomop > -1: + ,maxhomop=$maxhomop + #end if + #if $criteria > -1: + ,criteria=$criteria + #end if + #if $optimize: + ,optimize=$optimize + #end if + #if $qfile_in: + ,qfile=$qfile_in + #end if + #if $names_in: + ,name=$names_in + #end if + #if $groups_in: + ,group=$groups_in + #end if + #if $alignreport_in: + ,alignreport=$alignreport_in + #end if + #if $taxonomy_in: + ,taxonomy=$taxonomy_in + #end if + #if $count_in: + ,count=$count_in + #end if + #if $summary: + ,summary=$summary + #end if + #if $contigsreport: + ,contigsreport=$contigsreport + #end if + ,processors='"\${GALAXY_SLOTS:-8}"' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur && + + ## move output files to correct destination + mv mothur.*.logfile "$logfile" && + prefix="$fasta_in" && + mv \${prefix%.dat}*.good.* "$fasta_out" && + mv \${prefix%.dat}*.bad.accnos "$bad_accnos" + #if $qfile_in: + && prefix="$qfile_in" && mv \${prefix%.dat}*.good.* "$qfile_out" + #end if + #if $names_in: + && prefix="$names_in" && mv \${prefix%.dat}*.good.* "$names_out" + #end if + #if $groups_in: + && prefix="$groups_in" && mv \${prefix%.dat}*.good.* "$groups_out" + #end if + #if $alignreport_in: + && prefix="$alignreport_in" && mv \${prefix%.dat}*.good.* "$alignreport_out" + #end if + #if $taxonomy_in: + && prefix="$taxonomy_in" && mv \${prefix%.dat}*.good.* "$taxonomy_out" + #end if + #if $count_in: + && prefix="$count_in" && mv \${prefix%.dat}*.good.* "$count_out" + #end if + ]]></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 - allows you to enter the summary file created by summary.seqs to save processing time when screening with parameters in the summary file"/> + <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - 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> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/> + <data name="fasta_out" format_source="fasta_in" label="${tool.name} on ${on_string}: good.${fasta_in.datatype.file_ext}"/> + <data name="bad_accnos" format="mothur.accnos" label="${tool.name} on ${on_string}: bad.accnos"/> + <data name="qfile_out" format_source="qfile_in" label="${tool.name} on ${on_string}: qfile"> + <filter>qfile_in</filter> + </data> + <data name="names_out" format="mothur.names" label="${tool.name} on ${on_string}: names"> + <filter>names_in</filter> + </data> + <data name="groups_out" format="mothur.groups" label="${tool.name} on ${on_string}: groups"> + <filter>groups_in</filter> + </data> + <data name="alignreport_out" format="mothur.align.report" label="${tool.name} on ${on_string}: align.report"> + <filter>alignreport_in</filter> + </data> + <data name="count_out" format="count" label="${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"/> + <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"/> + <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> + <expand macro="logfile-test"/> + </test> + <test> + <param name="fasta_in" value="amazon.fasta"/> + <param name="count_in" value="amazon.count_table"/> + <param name="maxambig" value="0"/> + <param name="maxlength" value="275"/> + <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e"/> + <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee"/> + <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documenation** + +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: http://www.mothur.org/wiki/Name_file +.. _group: http://www.mothur.org/wiki/Group_file +.. _align.report: http://www.mothur.org/wiki/Align.seqs +.. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs + +]]> + </help> + <expand macro="citations"/> +</tool>