Mercurial > repos > iuc > transit_resampling

annotate transit_resampling.xml @ 1:1d1ca6b30fbb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
author iuc
date Wed, 27 Feb 2019 10:14:26 -0500
parents 8ccb1b841efb
children b33af081b02e
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8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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1 <?xml version="1.0"?>
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1d1ca6b30fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
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2 <tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy1">
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8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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3 <description>- determine per-gene p-values</description>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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4 <macros>
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5 <import>macros.xml</import>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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6 </macros>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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7 <expand macro="requirements" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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8 <command detect_errors="exit_code"><![CDATA[
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9 @LINK_INPUTS@
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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10 #set $control_files = ','.join(['control_file_%d.wig' % idx for idx, _ in enumerate(str($controls).split(','))])
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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11 #for idx, filename in enumerate(str($controls).split(',')):
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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12 ln -s '$filename' control_file_${idx}.wig &&
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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13 #end for
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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14 transit resampling $input_files $control_files annotation.dat transit_out.txt
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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15 @STANDARD_OPTIONS@
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16 -s $samples -n $normalization $histogram $adaptive $exclude_zero $pseudo $loess
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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17 ]]>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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18 </command>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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19 <inputs>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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20 <expand macro="standard_inputs">
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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21 <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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22 <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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23 <param name="normalization" argument="-n" type="select" label="Normalization method">
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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24 <option value="TTR">TTR</option>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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25 </param>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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26 <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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27 <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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28 <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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29 <param name="pseudo" argument="-pc" type="boolean" truevalue="-pc" falsevalue="" label="Add pseudocounts at each site" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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30 <param name="loess" argument="-l" type="boolean" truevalue="-l" falsevalue="" label="Perform LOESS Correction" help="Helps remove possible genomic position bias." />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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31
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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32 </expand>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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33 </inputs>
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34 <outputs>
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35 <expand macro="outputs" />
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36 </outputs>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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37 <tests>
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38 <test>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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39 <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
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40 <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" />
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41 <param name="annotation" ftype="gff3" value="transit-in1.gff3" />
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42 <param name="samples" value="1000" />
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43 <param name="burnin" value="100" />
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44 <output name="sites" file="resampling-sites1.txt" ftype="tabular" compare="sim_size" />
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45 </test>
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46 </tests>
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47 <help>
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48 <![CDATA[
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49 The re-sampling method is a comparative analysis the allows that can be used to determine conditional essentiality of genes. It is based on a permutation test, and is capable of determining read-counts that are significantly different across conditions.
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50 ]]></help>
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51 <expand macro="citations" />
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52 </tool>