Mercurial > repos > sanbi-uwc > mothur_test
diff tools/mothur/get.seqs.xml @ 0:ee4fee239fe7 draft default tip
planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 03 Jun 2016 09:32:47 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mothur/get.seqs.xml Fri Jun 03 09:32:47 2016 -0400 @@ -0,0 +1,178 @@ +<tool profile="16.07" id="mothur_get_seqs" name="Get.seqs" version="@WRAPPER_VERSION@.0"> + <description>Picks sequences by name</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + echo 'get.seqs( + accnos=$accnos, + #if $fasta_in: + fasta=$fasta_in, + #end if + #if $fastq_in: + fastq=$fastq_in, + #end if + #if $count_in: + count=$count_in, + #end if + #if $qfile_in: + qfile=$qfile_in, + #end if + #if $name_in: + name=$name_in, + #end if + #if $group_in: + group=$group_in, + #end if + #if $alignreport_in: + alignreport=$alignreport_in, + #end if + #if $list_in: + list=$list_in, + #end if + #if $taxonomy_in: + taxonomy=$taxonomy_in, + #end if + dups=$dups + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur && + + ## move output files to correct destination + mv mothur.*.logfile "$logfile" + + #if $fasta_in: + && prefix='$fasta_in' + && mv \${prefix%.dat}*.pick.* "$fasta_out" + #end if + #if $fastq_in: + && prefix='$fastq_in' + && mv \${prefix%.dat}*.pick.* "$fastq_out" + #end if + #if $count_in: + && prefix='$count_in' + && mv \${prefix%.dat}*.pick.* "$count_out" + #end if + #if $qfile_in: + && prefix='$qfile_in' + && mv \${prefix%.dat}*.pick.* "$qfile_out" + #end if + #if $name_in: + && prefix='$name_in' + && mv \${prefix%.dat}*.pick.* "$name_out" + #end if + #if $group_in: + && prefix='$group_in' + && mv \${prefix%.dat}*.pick.* "$group_out" + #end if + #if $alignreport_in: + && prefix='$alignreport_in' + && mv \${prefix%.dat}*.pick.* "$alignreport_out" + #end if + #if $list_in: + && prefix='$list_in' + && mv \${prefix%.dat}*.pick.* "$list_out" + #end if + #if $taxonomy_in: + && prefix='$taxonomy_in' + && mv \${prefix%.dat}*.pick.* "$taxonomy_out" + #end if + ]]></command> + <inputs> + <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/> + <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> + <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> + <param name="fastq_in" type="data" format="fastq" optional="true" label="count - a count_table" help="fastq - allows you to select sequences from your fastq file"/> + <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> + <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/> + <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> + <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> + <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> + <param name="dups" type="boolean" truevalue="dups" falsevalue="false" checked="true" label="dups - Apply to duplicates"/> + </inputs> + <outputs> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/> + <data name="fasta_out" format_source="fasta_in" label="${tool.name} on ${on_string}: pick.fasta"> + <filter>fasta_in</filter> + </data> + <data name="fastq_out" format_source="fastq_in" label="${tool.name} on ${on_string}: pick.fastq"> + <filter>fastq_in</filter> + </data> + <data name="count_out" format_source="count_in" label="${tool.name} on ${on_string}: pick.count"> + <filter>count_in</filter> + </data> + <data name="qfile_out" format_source="qfile_in" label="${tool.name} on ${on_string}: pick.qfile"> + <filter>qfile_in</filter> + </data> + <data name="name_out" format="mothur.names" label="${tool.name} on ${on_string}: pick.names"> + <filter>name_in</filter> + </data> + <data name="group_out" format="mothur.groups" label="${tool.name} on ${on_string}: pick.groups"> + <filter>group_in</filter> + </data> + <data name="alignreport_out" format="mothur.align.report" label="${tool.name} on ${on_string}: pick.align.report"> + <filter>alignreport_in</filter> + </data> + <data name="list_out" format="mothur.list" label="${tool.name} on ${on_string}: pick.list"> + <filter>list_in</filter> + </data> + <data name="taxonomy_out" format="mothur.seq.taxonomy" label="${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=""/> + <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/> + <expand macro="logfile-test"/> + </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"/> + <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/> + <expand macro="logfile-test"/> + </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="false"/> + <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/> + <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/> + <expand macro="logfile-test"/> + </test> + <test> + <param name="accnos" value="amazon.bad.accnos"/> + <param name="count_in" value="amazon.count_table"/> + <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documenation** + +The get.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 contains only the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection. + +.. _name: http://www.mothur.org/wiki/Name_file +.. _group: http://www.mothur.org/wiki/Group_file +.. _list: http://www.mothur.org/wiki/List_file +.. _align.report: http://www.mothur.org/wiki/Align.seqs +.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline +.. _list.seqs: http://www.mothur.org/wiki/list.seqs +.. _get.seqs: http://www.mothur.org/wiki/Get.seqs + +v.1.27.0 : Updated to Mothur 1.33, added count and fastq params +]]> + </help> + <expand macro="citations"/> +</tool>