Mercurial > repos > iuc > mothur_chimera_check
diff chimera.check.xml @ 2:37bd32018025 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:20:22 -0400 |
parents | 8e874c18a298 |
children |
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--- a/chimera.check.xml Tue Sep 05 17:15:20 2017 -0400 +++ b/chimera.check.xml Tue Mar 20 22:20:22 2018 -0400 @@ -7,63 +7,65 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && - ln -s "$alignment.template" alignment.template.dat && - #if $svg.gen == "yes": - ln -s "$svg.name" svg.name.dat && - #end if +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$alignment.reference' alignment.reference.dat && +#if $svg_cond.svg == "yes": + ln -s '$svg_cond.name' svg.name.dat && +#end if - echo 'chimera.check( - fasta=fasta.dat, - reference=alignment.template.dat, - #if $svg.gen == "yes": - svg=yes, - name=svg.name.dat, - #end if - increment=$increment, - ksize=$ksize, - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'chimera.check( + fasta=fasta.dat, + reference=alignment.reference.dat, + #if $svg_cond.svg == "yes": + svg=yes, + name=svg.name.dat, + #end if + increment=$increment, + ksize=$ksize, + 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" argument="fasta" label="fasta - Candiate Aligned Sequences"/> + <param argument="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=""> + <param name="source" type="select" label="Select Reference Template from"> <option value="hist">History</option> <option value="ref">Cached Reference</option> </param> <when value="ref"> - <param name="template" type="select" argument="reference" label="reference - Select an alignment database" help=""> - <options from_data_table="mothur_aligndb"> - </options> + <param argument="reference" type="select" label="reference - Select an alignment database"> + <options from_data_table="mothur_aligndb"/> </param> </when> <when value="hist"> - <param name="template" type="data" format="fasta" argument="reference" label="reference - Reference to align with" help=""/> + <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/> </when> </conditional> - <param name="ksize" type="integer" value="7" argument="ksize" label="ksize - kmer length to determine differences between sequence fragments (uses default if < 1)"/> - <param name="increment" type="integer" value="10" argument="increment" label="increment - Increment for window slide on each iteration (uses default if < 1)" help="Default is 10, but you may set it up to sequence length minus twice the window."/> - <conditional name="svg"> - <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help=""> + <param argument="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments" + help="uses default if < 1"/> + <param argument="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration" + help="Default is 10, but you may set it up to sequence length minus twice the window."/> + <conditional name="svg_cond"> + <param argument="svg" type="select" label="svg - Generate a SVG plot for each query sequence"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> - <param name="name" type="data" format="mothur.names" optional="true" argument="name" label="name - Names of queries for which to generate SVG plot"/> + <param argument="name" type="data" format="mothur.names" optional="true" label="name - Names of queries for which to generate SVG plot"/> </when> </conditional> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> - <data name="out_file" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/> + <data name="chimeracheck.chimeras" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/> <collection name="images" type="list" label="${tool.name} on ${on_string}: SVG images"> <discover_datasets pattern="(?P<designation>.*)\.chimeracheck\.svg"/> <filter>svg['gen'] == 'yes'</filter> @@ -73,26 +75,27 @@ <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" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> + <param name="reference" value="HMP_MOCK.v35.align"/> + <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <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"/> - <param name="gen" value="yes"/> + <param name="reference" value="HMP_MOCK.v35.align"/> + <param name="svg" value="yes"/> <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny"/> - <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> + <output name="chimeracheck.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/> <output_collection name="images" count="2"> <element name="M00967_43_000000000-A3JHG_1_1101_14010_4122" file="M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg"/> <element name="M00967_43_000000000-A3JHG_1_1101_13293_4703" md5="0d99dc17c183dab4efc75c697060a9a5"/> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -104,7 +107,6 @@ .. _chimera.check: https://www.mothur.org/wiki/Chimera.check -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>