Mercurial > repos > iuc > mothur_remove_seqs
diff remove.seqs.xml @ 2:0b8ca0026f28 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:12:08 -0400 |
| parents | e59ddb750b65 |
| children | d38f2ac5db71 |
line wrap: on
line diff
--- a/remove.seqs.xml Tue Sep 05 16:57:34 2017 -0400 +++ b/remove.seqs.xml Tue Mar 20 22:12:08 2018 -0400 @@ -7,87 +7,87 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@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 && +## 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 + 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"/> @@ -101,6 +101,7 @@ <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"/> @@ -137,34 +138,62 @@ <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" md5="2357e1429647afbe21521a60935919bf"/> + <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" md5="1e10d0793f1c5f12388156d5922c0eb8"/> + <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" md5="2357e1429647afbe21521a60935919bf"/> - <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/> + <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" md5="bd1cb7af6f277210c5c11ff7d7c54592"/> + <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[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -179,7 +208,7 @@ .. _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> + + ]]></help> <expand macro="citations"/> </tool>