Mercurial > repos > iuc > humann2_rna_dna_norm

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author iuc
date Tue, 01 Aug 2017 07:56:14 -0400
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children 6893a2b1da17
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c8ef30c8451d planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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1 <tool id="humann2_rna_dna_norm" name="Normalize" version="@WRAPPER_VERSION@.0">
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2 <description> combined meta'omic sequencing data</description>
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3 <macros>
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4 <import>humann2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 humann2_rna_dna_norm
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10 --input_dna '$input_dna'
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11 --input_rna '$input_rna'
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12 --output_basename 'results'
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13 --method '$method'
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14 #if $log.log_transform == 'yes'
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15 --log_transform
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16 --log_base $log.log_base
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17 #end if
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18 ]]></command>
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19 <inputs>
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20 <param argument="--input_dna" type="data" format="tsv,tabular,biom1" label="Original DNA output table"/>
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21 <param argument="--input_rna" type="data" format="tsv,tabular,biom1" label="Original RNA output table"/>
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22 <param argument="--method" type="select" label="Choice of smoothing method">
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23 <option value="laplace">Laplace</option>
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24 <option value="witten_bell">Witten-Bell</option>
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25 </param>
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26 <conditional name="log">
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27 <param argument="--log_transform" type="select" label="Report log-transformed relative expression values?">
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28 <option value="yes">Yes</option>
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29 <option value="no">No</option>
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30 </param>
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31 <when value="yes">
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32 <param argument="--log_base" type="integer" value="2" label="Base for log transformation"/>
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33 </when>
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34 <when value="no"/>
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35 </conditional>
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36 </inputs>
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37 <outputs>
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38 <data format="tsv" name="results-relative_expression" from_work_dir="results-relative_expression.tsv" label="${tool.name} on ${on_string}: normalized RNA"/>
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39 <data format="tsv" name="results-smoothed_dna" from_work_dir="results-smoothed_dna.tsv" label="${tool.name} on ${on_string}: smoothed DNA"/>
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40 <data format="tsv" name="results-smoothed_rna" from_work_dir="results-smoothed_rna.tsv" label="${tool.name} on ${on_string}: smoothed RNA"/>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input_dna" value="rna_dna_norm-dna.txt"/>
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45 <param name="input_rna" value="rna_dna_norm-rna.txt"/>
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46 <param name="method" value="laplace"/>
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47 <conditional name="log">
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48 <param name="log_transform" value="no"/>
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49 </conditional>
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50 <output name="results-relative_expression" md5="193000abf357cb14f70273ba6cd5f095"/>
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51 <output name="results-smoothed_dna" md5="3767aa13988a4dca40a07cb6970bcc60"/>
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52 <output name="results-smoothed_rna" md5="8b1bcb819c31ef0ba5ab4975582bfcf7"/>
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53 </test>
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54 <test>
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55 <param name="input_dna" value="rna_dna_norm-dna.txt"/>
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56 <param name="input_rna" value="rna_dna_norm-rna.txt"/>
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57 <param name="method" value="witten_bell"/>
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58 <conditional name="log">
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59 <param name="log_transform" value="yes"/>
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60 <param name="log_base" value="2"/>
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61 </conditional>
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62 <output name="results-relative_expression" md5="3064e6377c074c6e6e9cf7fdfd466ec9"/>
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63 <output name="results-smoothed_dna" md5="3a1203c0986d79e9cb4ac0e3a4a89f4e"/>
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64 <output name="results-smoothed_rna" md5="1038b44e52b95a867dc6341b4dd91697"/>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 @HELP_HEADER@
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69
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70 Given a DNA table and a RNA table, produce smoothed RNA and DNA values as well as relative expression values. "Smoothing" means substituting a small value in place of a zero or missing value. The default method used is "Laplace" (pseudocount) scaling, where the pseudocount is the sample-specific minimum non-zero value. (Witten-Bell smoothing is also implemented.)
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71 ]]></help>
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72 <expand macro="citations"/>
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73 </tool>