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1 <tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.1">
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2 <description> for multiple (>2) species alignments</description>
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3 <command interpreter="perl">
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4 multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl
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5 $input1
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6 $out_file1
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7 $thresholds
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8 $species
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9 "$treedefinition"
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10 $separation
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11
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12 </command>
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13 <inputs>
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14 <page>
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15 <param format="maf" name="input1" type="data" label="Select MAF alignments"/>
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16 <param name="separation" size="10" type="integer" value="10" label="Minimum base pair distance between adjacent microsatellite blocks"
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17 help="A value of 10 means: Adjacent microsatellites separated by less than 10 base pairs will be excluded from the output."/>
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18 <param name="thresholds" size="15" type="text" value="9,10,12,12" label="Minimum Threshold for the number of repeats for microsatellites"
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19 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."/>
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20 <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">
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21 <options>
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22 <filter type="data_meta" ref="input1" key="species" />
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23 </options>
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24 </param>
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25 <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"
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26 help="For example: ((((hg18,panTro2),ponAbe2),rheMac2),calJac1)"/>
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27 </page>
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28 </inputs>
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29 <outputs>
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30 <data format="txt" name="out_file1" metadata_source="input1"/>
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31 </outputs>
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32 <requirements>
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33 <requirement type="binary">sputnik</requirement>
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34 </requirements>
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35 <tests>
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36 <test>
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37 <param name="input1" value="chr22_5sp.maf"/>
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38 <param name="thresholds" value="9,10,12,12"/>
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39 <param name="species" value="hg18,panTro2,ponAbe2,rheMac2,calJac1"/>
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40 <param name="treedefinition" value="((((hg18, panTro2), ponAbe2), rheMac2), calJac1)"/>
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41 <param name="separation" value="10"/>
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42 <output name="out_file1" file="chr22_5sp.microraw.tabular"/>
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43 </test>
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44 </tests>
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45
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46 <help>
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47
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48 .. class:: infomark
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49
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50 **What it does**
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51
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52 This tool finds ortholgous microsatellite blocks between aligned species
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53
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54 </help>
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55
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56
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57 </tool>
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