Mercurial > repos > iuc > mothur_sffinfo
diff sffinfo.xml @ 0:5ada2d00e874 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:34:03 -0400 |
| parents | |
| children | 13d1e5e44a91 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sffinfo.xml Fri May 19 05:34:03 2017 -0400 @@ -0,0 +1,119 @@ +<tool profile="16.07" id="mothur_sffinfo" name="Sffinfo" version="@WRAPPER_VERSION@.0"> + <description>Summarize the quality of sequences</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 "$sff" sff.dat && + ln -s "$accnos" accnos.dat && + #if $oligo.add == "yes": + ln -s "$oligo.oligos" oligo.oligos.dat && + #end if + + echo 'sffinfo( + sff=sff.dat, + fasta=$fasta, + qfile=$qfile, + $sfftxt + flow=$flow, + trim=$trim + #if $accnos: + ,accnos=accnos.dat + #end if + #if $oligo.add == "yes": + ,oligos=oligo.oligos.dat + ,bdiffs=$oligo.bdiffs + ,pdiffs=$oligo.pdiffs + ,tdiffs=$oligo.tdiffs + ,ldiffs=$oligo.ldiffs + ,sdiffs=$oligo.sdiffs + #end if + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="sff" type="data" format="sff" label="sff - Sff data"/> + <conditional name="oligo"> + <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words "forward", "reverse", and "barcode" or it can start with a "#" to tell mothur to ignore that line of the oligos file."> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/> + <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/> + <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/> + <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/> + <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/> + <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/> + </when> + </conditional> + <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fasta - Add fasta to your history"/> + <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/> + <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/> + <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/> + <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/> + <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"> + <filter>fasta</filter> + </data> + <data name="out_qfile" format="qual454" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual"> + <filter>qfile</filter> + </data> + <data name="out_sfftxt" format="txt" from_work_dir="sff*.sff.txt" label="${tool.name} on ${on_string}: sff.txt"> + <filter>sfftxt</filter> + </data> + <data name="out_flow" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flowgram"> + <filter>flow</filter> + </data> + <data name="out_scrap" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap.sff"> + <filter>oligo['add'] == 'yes'</filter> + </data> + </outputs> + <tests> + <test><!-- test without oligos --> + <param name="sff" value="Fasting_Example1.sff"/> + <param name="sfftxt" value="true"/> + <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/> + <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/> + <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/> + <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with oligos file --> + <param name="sff" value="Fasting_Example1.sff"/> + <param name="add" value="yes"/> + <param name="oligos" value="GQY1XT001.oligos"/> + <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/> + <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/> + <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/> + <output name="out_scrap" md5="f03c422fe364815e7214ad31ad135aca" ftype="sff"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. + + +.. _sffinfo: https://www.mothur.org/wiki/Sffinfo +]]> + </help> + <expand macro="citations"/> +</tool>