Mercurial > repos > xuebing > sharplabtool
view tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml @ 0:9071e359b9a3
Uploaded
author | xuebing |
---|---|
date | Fri, 09 Mar 2012 19:37:19 -0500 |
parents | |
children |
line wrap: on
line source
<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.1"> <description> for multiple (>2) species alignments</description> <command interpreter="perl"> multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl $input1 $out_file1 $thresholds $species "$treedefinition" $separation </command> <inputs> <page> <param format="maf" name="input1" type="data" label="Select MAF alignments"/> <param name="separation" size="10" type="integer" value="10" label="Minimum base pair distance between adjacent microsatellite blocks" help="A value of 10 means: Adjacent microsatellites separated by less than 10 base pairs will be excluded from the output."/> <param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites" help="A value of 9,10,12,12 means: All monos having fewer than 9 repeats, dis having fewer than 5 repeats, tris having fewer than 4 repeats, tetras having fewer than 3 repeats will be excluded from the output."/> <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="NOTE: Currently users are requested to select one of these three combinations: hg18-panTro2-ponAbe2, hg18-panTro2-ponAbe2-rheMac2 or hg18-panTro2-ponAbe2-rheMac2-calJac1"> <options> <filter type="data_meta" ref="input1" key="species" /> </options> </param> <param name="treedefinition" size="200" type="text" value = "((((hg18,panTro2),ponAbe2),rheMac2),calJac1)" label="Tree definition of all species above whether or not selected for microsatellite extraction" help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/> </page> </inputs> <outputs> <data format="txt" name="out_file1" metadata_source="input1"/> </outputs> <requirements> <requirement type="binary">sputnik</requirement> </requirements> <tests> <test> <param name="input1" value="chr22_5sp.maf"/> <param name="thresholds" value="9,10,12,12"/> <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/> <param name="treedefinition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/> <param name="separation" value="10"/> <output name="out_file1" file="chr22_5sp.microraw.tabular"/> </test> </tests> <help> .. class:: infomark **What it does** This tool finds ortholgous microsatellite blocks between aligned species </help> </tool>