Mercurial > repos > iuc > structureharvester

annotate structureharvester.xml @ 0:8a7390c4d6bf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
author iuc
date Mon, 11 Dec 2017 04:37:17 -0500
parents
children 8dc371b783eb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
1 <tool id="structureharvester" name="structureHarvester" version="0.6.94">
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
2 <description>for parsing STRUCTURE outputs and for performing the Evanno method</description>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
3 <requirements>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
4 <requirement type="package" version="0.6.94">structureharvester</requirement>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
5 </requirements>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
6 <version_command><![CDATA[
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
7 structureHarvester.py --version
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
8 ]]></version_command>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
10 mkdir inputs &&
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
11 #for $input in $inputs
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
12 ln -s '$input' 'inputs/$input.element_identifier' &&
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
13 #end for
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
14 structureHarvester.py --dir inputs/ --out . $evanno $clumpp &&
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
15 mv summary.txt '$summary'
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
16 #if $evanno
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
17 && mv evanno.txt $evanno
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
18 #end if
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
19 #if $clumpp
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
20 && mkdir clumpp_indfile clumpp_popfile
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
21 && mv *.indfile clumpp_indfile/
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
22 && mv *.popfile clumpp_popfile/
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
23 #end if
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
24 ]]></command>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
25 <inputs>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
26 <param name="inputs" type="data" format="txt" multiple="true" label="STRUCTURE outputs" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
27 <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."/>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
28 <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." />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
29 </inputs>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
30 <outputs>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
31 <data name="summary" format="txt" label="Structure Harvester summary"/>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
32 <data name="evanno" format="txt" label="Evann method output">
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
33 <filter>evanno</filter>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
34 </data>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
35 <collection name="clumpp_indfile" type="list" label="Clumpp K*.indfile">
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
36 <filter>clumpp</filter>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
37 <discover_datasets pattern="__name__" format="txt" directory="clumpp_indfile" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
38 </collection>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
39 <collection name="clumpp_popfile" type="list" label="Clumpp K*.popfile">
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
40 <filter>clumpp</filter>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
41 <discover_datasets pattern="__name__" format="txt" directory="clumpp_popfile" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
42 </collection>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
43 </outputs>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
44 <tests>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
45 <test>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
46 <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" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
47 <param name="evanno" value="false" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
48 <param name="clumpp" value="true" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
49 <output name="summary">
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
50 <assert_contents>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
51 <has_line line="1&#009;2&#009;-4329.950000&#009;0.070711" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
52 <has_line line="4&#009;2&#009;-2773.550000&#009;0.212132" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
53 <has_line line="K1ReRun_run_2_f&#009;2&#009;1&#009;-4330.0&#009;-4300.2&#009;59.7" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
54 <has_line line="Admix_run_008_f&#009;008&#009;4&#009;-2773.4&#009;-2678.8&#009;189.2" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
55 <has_line line="Core version: vA.2 July 2014" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
56 </assert_contents>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
57 </output>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
58 <output_collection name="clumpp_indfile" type="list">
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
59 <element name="K1.indfile" value="clumpp_indfile/K1.indfile" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
60 <element name="K4.indfile" value="clumpp_indfile/K4.indfile" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
61 </output_collection>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
62 <output_collection name="clumpp_popfile" type="list">
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
63 <element name="K1.popfile" value="clumpp_popfile/K1.popfile" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
64 <element name="K4.popfile" value="clumpp_popfile/K4.popfile" />
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
65 </output_collection>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
66 </test>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
67 </tests>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
68 <help><![CDATA[
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
69
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
70 Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method.
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
71
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
72 .. _Structure_Harvester: http://taylor0.biology.ucla.edu/structureHarvester/
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
73 .. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
74
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
75 ]]></help>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
76 <citations>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
77 <citation type="doi">10.1007/s12686-011-9548-7</citation>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
78 <citation type="doi">10.1111/j.1365-294X.2005.02553.x</citation>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
79 <citation type="doi">10.1093/bioinformatics/btm233</citation>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
80 </citations>
8a7390c4d6bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit 8375ca4822c039d051473b38801066b8a9c1edc7
iuc
parents:
diff changeset
81 </tool>