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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author | iuc |
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date | Mon, 17 Jun 2024 12:22:09 +0000 |
parents | 0b8ca0026f28 |
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<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="biotools"/> <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 $dups )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log #end if ]]></command> <inputs> <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names of sequences to be removed"/> <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> <param name="fastq_in" type="data" format="fastq" optional="true" label="fastq"/> <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/> <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${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=""/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> <output name="fasta_out"> <assert_contents> <expand macro="test-fasta-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> </assert_contents> </output> </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"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> <output name="fastq_out"> <assert_contents> <expand macro="test-fastq-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> </assert_contents> </output> </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"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> <output name="fasta_out"> <assert_contents> <expand macro="test-fasta-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> </assert_contents> </output> <output name="fastq_out"> <assert_contents> <expand macro="test-fastq-format"/> <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> </assert_contents> </output> </test> <test> <param name="accnos" value="amazon.bad.accnos"/> <param name="count_in" value="amazon.count_table"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> <output name="count_out"> <assert_contents> <expand macro="test-count-format"/> <has_text text="U68595"/> </assert_contents> </output> </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>