Mercurial > repos > iuc > mothur_sort_seqs
diff sort.seqs.xml @ 0:a8653fd1ca73 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:30:16 -0400 |
| parents | |
| children | 6619e67b064d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sort.seqs.xml Fri May 19 05:30:16 2017 -0400 @@ -0,0 +1,132 @@ +<tool profile="16.07" id="mothur_sort_seqs" name="Sort.seqs" version="@WRAPPER_VERSION@.0"> + <description>put sequences in different files in the same order</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + ## create symlinks to input datasets + ln -s "$fasta_in" fasta_in.dat && + ln -s "$qfile_in" qfile_in.dat && + ln -s "$flow_in" flow_in.dat && + ln -s "$name_in" name_in.dat && + ln -s "$group_in" group_in.dat && + ln -s "$tax_in" tax_in.dat && + ln -s "$accnos" accnos.dat && + ln -s "$count" count.dat && + + echo 'sort.seqs( + #if $fasta_in: + fasta=fasta_in.dat, + #end if + #if $qfile_in: + qfile=qfile_in.dat, + #end if + #if $flow_in: + flow=flow_in.dat, + #end if + #if $name_in: + name=name_in.dat, + #end if + #if $group_in: + group=group_in.dat, + #end if + #if $tax_in: + taxonomy=tax_in.dat, + #end if + #if $accnos: + accnos=accnos.dat, + #end if + #if $count: + count=count.dat, + #end if + large=$large + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/> + <param name="qfile_in" type="data" format="qual454" optional="true" label="qfile - sequence quality" help="format must be qual454"/> + <param name="flow_in" type="data" format="mothur.sff.flow" optional="true" label="flow - sff flowgram" help="format must be mothur.sff.flow"/> + <param name="group_in" type="data" format="mothur.groups" optional="true" label="groups - sequence groupings" help="format must be mothur.groups"/> + <param name="name_in" type="data" format="mothur.names" optional="true" label="names - name reference" help="format must be mothur.names"/> + <param name="tax_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - taxonomy reference" help="format must be mothur.seq.taxonomy"/> + <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/> + <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="format must be mothur.count_table (generated by count.seqs)"/> + <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.fasta"> + <filter>fasta_in</filter> + </data> + <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.qfile"> + <filter>qfile_in</filter> + </data> + <data name="flow_out" format_source="flow_in" from_work_dir="flow_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.flow"> + <filter>flow_in</filter> + </data> + <data name="group_out" format_source="group_in" from_work_dir="group_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.group"> + <filter>group_in</filter> + </data> + <data name="name_out" format_source="name_in" from_work_dir="name_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.name"> + <filter>name_in</filter> + </data> + <data name="taxonomy_out" format_source="tax_in" from_work_dir="tax_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.taxonomy"> + <filter>tax_in</filter> + </data> + </outputs> + <tests> + <test> + <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> + <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> + <expand macro="logfile-test"/> + </test> + <test> + <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> + <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/> + <expand macro="logfile-test"/> + </test> + <test> + <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> + <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> + <expand macro="logfile-test"/> + </test> + <test> + <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> + <param name="count" value="amazon.count_table" ftype="mothur.count_table"/> + <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with multiple file types input --> + <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> + <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> + <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> + <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> + <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/> + <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order. +You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads. + +.. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs + +]]> + </help> + <expand macro="citations"/> +</tool>