Mercurial > repos > iuc > structureharvester
diff structureharvester.xml @ 0:8a7390c4d6bf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
author | iuc |
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date | Mon, 11 Dec 2017 04:37:17 -0500 |
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children | 8dc371b783eb |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/structureharvester.xml Mon Dec 11 04:37:17 2017 -0500 @@ -0,0 +1,81 @@ +<tool id="structureharvester" name="structureHarvester" version="0.6.94"> + <description>for parsing STRUCTURE outputs and for performing the Evanno method</description> + <requirements> + <requirement type="package" version="0.6.94">structureharvester</requirement> + </requirements> + <version_command><![CDATA[ + structureHarvester.py --version + ]]></version_command> + <command detect_errors="exit_code"><![CDATA[ + mkdir inputs && + #for $input in $inputs + ln -s '$input' 'inputs/$input.element_identifier' && + #end for + structureHarvester.py --dir inputs/ --out . $evanno $clumpp && + mv summary.txt '$summary' + #if $evanno + && mv evanno.txt $evanno + #end if + #if $clumpp + && mkdir clumpp_indfile clumpp_popfile + && mv *.indfile clumpp_indfile/ + && mv *.popfile clumpp_popfile/ + #end if + ]]></command> + <inputs> + <param name="inputs" type="data" format="txt" multiple="true" label="STRUCTURE outputs" /> + <param argument="--evanno" type="boolean" checked="false" truevalue="--evanno" falsevalue="" label="If possible, performs the Evanno 2005 method." help="You must test at least 3 values of K. K values must be sequential. The number of replicates per K > 1."/> + <param argument="--clumpp" type="boolean" checked="false" truevalue="--clumpp" falsevalue="" label="Generates one K*.indfile for each value of K run, for use with CLUMPP." /> + </inputs> + <outputs> + <data name="summary" format="txt" label="Structure Harvester summary"/> + <data name="evanno" format="txt" label="Evann method output"> + <filter>evanno</filter> + </data> + <collection name="clumpp_indfile" type="list" label="Clumpp K*.indfile"> + <filter>clumpp</filter> + <discover_datasets pattern="__name__" format="txt" directory="clumpp_indfile" /> + </collection> + <collection name="clumpp_popfile" type="list" label="Clumpp K*.popfile"> + <filter>clumpp</filter> + <discover_datasets pattern="__name__" format="txt" directory="clumpp_popfile" /> + </collection> + </outputs> + <tests> + <test> + <param name="inputs" value="example_harvester_archive/Admix_run_001_f,example_harvester_archive/Admix_run_002_f,example_harvester_archive/Admix_run_004_f,example_harvester_archive/Admix_run_005_f,example_harvester_archive/Admix_run_007_f,example_harvester_archive/Admix_run_008_f,example_harvester_archive/K1ReRun_run_1_f,example_harvester_archive/K1ReRun_run_2_f" /> + <param name="evanno" value="false" /> + <param name="clumpp" value="true" /> + <output name="summary"> + <assert_contents> + <has_line line="1	2	-4329.950000	0.070711" /> + <has_line line="4	2	-2773.550000	0.212132" /> + <has_line line="K1ReRun_run_2_f	2	1	-4330.0	-4300.2	59.7" /> + <has_line line="Admix_run_008_f	008	4	-2773.4	-2678.8	189.2" /> + <has_line line="Core version: vA.2 July 2014" /> + </assert_contents> + </output> + <output_collection name="clumpp_indfile" type="list"> + <element name="K1.indfile" value="clumpp_indfile/K1.indfile" /> + <element name="K4.indfile" value="clumpp_indfile/K4.indfile" /> + </output_collection> + <output_collection name="clumpp_popfile" type="list"> + <element name="K1.popfile" value="clumpp_popfile/K1.popfile" /> + <element name="K4.popfile" value="clumpp_popfile/K4.popfile" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ + +Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method. + +.. _Structure_Harvester: http://taylor0.biology.ucla.edu/structureHarvester/ +.. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html + + ]]></help> + <citations> + <citation type="doi">10.1007/s12686-011-9548-7</citation> + <citation type="doi">10.1111/j.1365-294X.2005.02553.x</citation> + <citation type="doi">10.1093/bioinformatics/btm233</citation> + </citations> +</tool>