Mercurial > repos > iuc > mothur_remove_seqs
diff remove.seqs.xml @ 0:e59ddb750b65 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:58:47 -0400 |
| parents | |
| children | 0b8ca0026f28 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/remove.seqs.xml Fri May 19 05:58:47 2017 -0400 @@ -0,0 +1,185 @@ +<tool profile="16.07" id="mothur_remove_seqs" name="Remove.seqs" version="@WRAPPER_VERSION@.0"> + <description>Remove sequences by name</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + ## if accnos file is empty, just output files as-is, mothur errors if accnos empty (e.g. chimera filtering in pipeline but sample had no chimeras) + #import os + #if $os.lstat(str($accnos)).st_size == 0: + echo "accnos file empty, nothing to remove, skipping step" + #if $fasta_in: + && cp $fasta_in $fasta_out + #end if + #if $fastq_in: + && cp $fastq_in $fastq_out + #end if + #if $count_in: + && cp $count_in $count_out + #end if + #if $qfile_in: + && cp $qfile_in $qfile_out + #end if + #if $name_in: + && cp $name_in $name_out + #end if + #if $group_in: + && cp $group_in $group_out + #end if + #if $alignreport_in: + && cp $alignreport_in $alignreport_out + #end if + #if $list_in: + && cp $list_in $list_out + #end if + #if $taxonomy_in: + && cp $taxonomy_in $taxonomy_out + #end if + #else: + ## create symlinks to input datasets + ln -s "$accnos" accnos.dat && + ln -s "$fasta_in" fasta_in.dat && + ln -s "$fastq_in" fastq_in.dat && + ln -s "$count_in" count_in.dat && + ln -s "$qfile_in" qfile_in.dat && + ln -s "$name_in" name_in.dat && + ln -s "$group_in" group_in.dat && + ln -s "$alignreport_in" alignreport_in.dat && + ln -s "$list_in" list_in.dat && + ln -s "$taxonomy_in" taxonomy_in.dat && + + echo 'remove.seqs( + accnos=accnos.dat + #if $fasta_in: + ,fasta=fasta_in.dat + #end if + #if $fastq_in: + ,fastq=fastq_in.dat + #end if + #if $count_in: + ,count=count_in.dat + #end if + #if $qfile_in: + ,qfile=qfile_in.dat + #end if + #if $name_in: + ,name=name_in.dat + #end if + #if $group_in: + ,group=group_in.dat + #end if + #if $alignreport_in: + ,alignreport=alignreport_in.dat + #end if + #if $list_in: + ,list=list_in.dat + #end if + #if $taxonomy_in: + ,taxonomy=taxonomy_in.dat + #end if + $dups + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + #end if + ]]></command> + <inputs> + <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names of sequences to be removed"/> + <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> + <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> + <param name="fastq_in" type="data" format="fastq" optional="true" label="fastq"/> + <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> + <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/> + <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> + <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> + <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> + <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta"> + <filter>fasta_in</filter> + </data> + <data name="fastq_out" format_source="fastq_in" from_work_dir="fastq_in.pick.dat" label="${tool.name} on ${on_string}: pick.fastq"> + <filter>fastq_in</filter> + </data> + <data name="count_out" format_source="count_in" from_work_dir="count_in.pick.dat" label="${tool.name} on ${on_string}: pick.count"> + <filter>count_in</filter> + </data> + <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in.pick.dat" label="${tool.name} on ${on_string}: pick.qfile"> + <filter>qfile_in</filter> + </data> + <data name="name_out" format="mothur.names" from_work_dir="name_in.pick.dat" label="${tool.name} on ${on_string}: pick.names"> + <filter>name_in</filter> + </data> + <data name="group_out" format="mothur.groups" from_work_dir="group_in.pick.dat" label="${tool.name} on ${on_string}: pick.groups"> + <filter>group_in</filter> + </data> + <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in.pick.dat" label="${tool.name} on ${on_string}: pick.align.report"> + <filter>alignreport_in</filter> + </data> + <data name="list_out" format="mothur.list" from_work_dir="list_in.pick.dat" label="${tool.name} on ${on_string}: pick.list"> + <filter>list_in</filter> + </data> + <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in.pick.dat" label="${tool.name} on ${on_string}: pick.taxonomy"> + <filter>taxonomy_in</filter> + </data> + </outputs> + <tests> + <test> + <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> + <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> + <param name="dups" value=""/> + <expand macro="logfile-test"/> + <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/> + </test> + <test> + <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> + <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> + <expand macro="logfile-test"/> + <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/> + </test> + <test><!-- test two input files --> + <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> + <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> + <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> + <param name="dups" value=",dups=false"/> + <expand macro="logfile-test"/> + <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/> + <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/> + </test> + <test> + <param name="accnos" value="amazon.bad.accnos"/> + <param name="count_in" value="amazon.count_table"/> + <expand macro="logfile-test"/> + <output name="count_out" md5="bd1cb7af6f277210c5c11ff7d7c54592"/> + </test> + <!-- TODO: make test for empty accnos file --> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The remove.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that does not contain the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection. + +.. _name: https://www.mothur.org/wiki/Name_file +.. _group: https://www.mothur.org/wiki/Group_file +.. _list: https://www.mothur.org/wiki/List_file +.. _align.report: https://www.mothur.org/wiki/Align.seqs +.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline +.. _list.seqs: https://www.mothur.org/wiki/list.seqs +.. _remove.seqs: https://www.mothur.org/wiki/Remove.seqs +]]> + </help> + <expand macro="citations"/> +</tool>