Mercurial > repos > dereeper > sniplay3
view MDSplot/mdsplot.xml @ 21:50bd37c444ac draft
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author | dereeper |
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date | Mon, 23 Mar 2015 05:35:48 -0400 |
parents | a0a95688cf17 |
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<tool id="sniplay_mdsplot" name="MDS plot" version="1.1.1"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> IBS matrix / multi-dimensional scaling</description> <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> <requirement type="package" version="0.1.13">plink</requirement> </requirements> <!-- [OPTIONAL] Command to be executed to get the tool's version string --> <version_command> <!-- tool_binary -v --> </version_command> <!-- [REQUIRED] The command to execute --> <command interpreter="bash"> mdsplot.sh $fileped $filemap $fileout_label $fileout_matrix $fileout_plot $fileout_log </command> <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="fileped" type="data" format="txt" optional="false" label="PED input" /> <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/> <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" /> </inputs> <!-- [REQUIRED] Output files --> <outputs> <data name="fileout_matrix" type="data" format="tabular" label="${fileout_label}.ibs_matrix.txt" /> <data name="fileout_plot" type="data" format="tabular" label="${fileout_label}.mds_plot.txt" /> <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> </outputs> <!-- [STRONGLY RECOMMANDED] Exit code rules --> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> <exit_code range="1:" level="fatal" /> </stdio> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> <param name="fileped" value="input.ped" /> <param name="filemap" value="input.map" /> <output name="fileout_matrix" file="output.ibs_matrix.txt" /> <output name="fileout_plot" file="output.mds_plot.txt" /> <output name="fileout_log" file="output.log" /> </test> <!-- [HELP] Multiple tests can be defined with different parameters --> <!-- <test> </test> --> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> <help> .. class:: infomark **Authors** --------------------------------------------------- .. class:: infomark **Please cite** If you use this tool, please cite dereeper et al. 2015 in prep. --------------------------------------------------- ======== MDS plot ======== ----------- Description ----------- Compute an IBS matrix and a multi-dimensional scaling. ----------------- Workflow position ----------------- **Upstream tools** =========== ========================== ======= Name output file(s) format =========== ========================== ======= =========== ========================== ======= **Downstream tools** =========== ========================== ======= Name output file(s) format =========== ========================== ======= =========== ========================== ======= ---------- Input file ---------- PED file MAP file 4 columns tabular file: chromosome, snp id, genetic distance, bp position ---------- Parameters ---------- Output name Output base name for the ouput files ------------ Output files ------------ Output_name.ibs_matrix.txt Tabular file with IBS matrix Output_name.mds_plot.txt File to construct mds plot Output_name.log Log file --------------------------------------------------- --------------- Working example --------------- Input files =========== PED file ----------- :: IRAT112 1 0 0 1 1 1 1 4 4 ... IAC25 1 0 0 1 1 1 1 4 4 ... CIRAD409 1 0 0 1 1 3 3 1 1 ... MAP file ----------- :: Chr1 Chr1:4299 0 4299 Chr1 Chr1:26710 0 26710 Chr1 Chr1:56184 0 56184 Chr1 Chr1:93272 0 93272 Parameters ========== Output name -> densities Output files ============ densities.ibs_matrix.txt ------------------------ :: Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE ... IRAT112 1 0.93691 0.937407 0.734724 0.943368 ... IAC25 0.93691 1 0.958768 0.723299 0.965723 ... densities.mds_plot.txt ---------------------- :: IRAT112 -0.0969382 0.0376036 IAC25 -0.0918126 0.0501177 </help> </tool>