Mercurial > repos > iuc > mothur_chimera_ccode
diff chimera.ccode.xml @ 0:3eca08ae427b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:14:11 -0400 |
parents | |
children | ad1b47de42a3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chimera.ccode.xml Fri May 19 05:14:11 2017 -0400 @@ -0,0 +1,129 @@ +<tool profile="16.07" id="mothur_chimera_ccode" name="Chimera.ccode" version="@WRAPPER_VERSION@.0"> + <description>Find putative chimeras using ccode</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 "$fasta" fasta.dat && + ln -s "$alignment.template" alignment.template.dat && + #if $mask.source2 == "history": + ln -s "$mask.input" mask.input.dat && + #end if + + echo 'chimera.ccode( + fasta=fasta.dat, + reference=alignment.template.dat, + filter=$filter, + #if $mask.source2 == "default": + mask=default, + #elif $mask.source2 == "history": + mask=mask.input.dat, + #end if + #if int($window) > 0: + window=$window, + #end if + #if int($numwanted) > 0: + numwanted=$numwanted, + #end if + processors='\${GALAXY_SLOTS:-8}' + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/> + <conditional name="alignment"> + <param name="source" type="select" label="Select Reference Template from" help=""> + <option value="hist">History</option> + <option value="ref">Cached Reference</option> + </param> + <when value="ref"> + <param name="template" type="select" label="reference - Select an alignment database" help=""> + <options from_data_table="mothur_aligndb"> + </options> + </param> + </when> + <when value="hist"> + <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> + </when> + </conditional> + <param name="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/> + <conditional name="mask"> + <param name="source2" type="select" label="Mask option"> + <option value="">None</option> + <option value="default">default ecoli mask</option> + <option value="history">From Your History</option> + </param> + <when value="history"> + <param name="input" type="data" format="mothur.filter" label="Mask for the reference file" help=""/> + </when> + <when value=""/> + <when value="default"/> + </conditional> + <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if < 1)" help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/> + <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="out_file" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/> + <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/> + <data name="mapinfo" format="tabular" from_work_dir="*.mapinfo" label="${tool.name} on ${on_string}: mapinfo"/> + </outputs> + <tests> + <test> + <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> + <param name="source" value="hist"/> + <param name="template" value="HMP_MOCK.v35.align"/> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/> + </assert_contents> + </output> + <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/> + <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/> + <expand macro="logfile-test"/> + </test> + <test> <!-- test with default ecoli mask --> + <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> + <param name="source" value="hist"/> + <param name="template" value="HMP_MOCK.v35.align"/> + <param name="source2" value="default"/> + <param name="window" value="100"/> + <output name="out_file" ftype="txt"> + <assert_contents> + <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/> + </assert_contents> + </output> + <output name="out_accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/> + <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The chimera.ccode_ command identifies putative chimeras using the ccode approach (Chimera and Cross-Over Detection and Evaluation). Ccode_ compares differences in distances, for each word, between query sequence and reference sequences, and reference sequences and themselves. + +This method was written using the algorithms described in the paper_ "Evaluating putative chimeric sequences from PCR-amplified products" by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez. + +The program can analyze sequences for any required word length. Generally, values of 5-20% of sequence length appear to deliver accurate results, for example, working on 16S rDNA sequences with a full-length of #1500 nt. It should be noted that the use of fragments either too long or too short might result in a reduction of sensitivity. + +.. _Ccode: http://www.microextreme.net/downloads.html +.. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf +.. _chimera.ccode: https://www.mothur.org/wiki/Chimera.ccode + +]]> + </help> + <expand macro="citations"/> +</tool>