Mercurial > repos > iuc > humann2_rna_dna_norm

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 8d953926efdf23d8c3fb8719341dff51a55a92f2"
author iuc
date Sun, 28 Mar 2021 07:01:39 +0000
parents 6893a2b1da17
children
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6893a2b1da17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
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1 <tool id="humann2_rna_dna_norm" name="Normalize" version="@WRAPPER_VERSION@.1">
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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>
4
6893a2b1da17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
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6 <expand macro="stdio"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 humann2_rna_dna_norm
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11 --input_dna '$input_dna'
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12 --input_rna '$input_rna'
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13 --output_basename 'results'
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14 --method '$method'
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15 #if $log.log_transform == 'yes'
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16 --log_transform
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17 --log_base $log.log_base
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18 #end if
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19 ]]></command>
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20 <inputs>
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21 <param argument="--input_dna" type="data" format="tsv,tabular,biom1" label="Original DNA output table"/>
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22 <param argument="--input_rna" type="data" format="tsv,tabular,biom1" label="Original RNA output table"/>
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23 <param argument="--method" type="select" label="Choice of smoothing method">
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24 <option value="laplace">Laplace</option>
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25 <option value="witten_bell">Witten-Bell</option>
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26 </param>
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27 <conditional name="log">
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28 <param argument="--log_transform" type="select" label="Report log-transformed relative expression values?">
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29 <option value="yes">Yes</option>
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30 <option value="no">No</option>
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31 </param>
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32 <when value="yes">
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33 <param argument="--log_base" type="integer" value="2" label="Base for log transformation"/>
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34 </when>
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35 <when value="no"/>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data format="tsv" name="results-relative_expression" from_work_dir="results-relative_expression.tsv" label="${tool.name} on ${on_string}: normalized RNA"/>
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40 <data format="tsv" name="results-smoothed_dna" from_work_dir="results-smoothed_dna.tsv" label="${tool.name} on ${on_string}: smoothed DNA"/>
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41 <data format="tsv" name="results-smoothed_rna" from_work_dir="results-smoothed_rna.tsv" label="${tool.name} on ${on_string}: smoothed RNA"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input_dna" value="rna_dna_norm-dna.txt"/>
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46 <param name="input_rna" value="rna_dna_norm-rna.txt"/>
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47 <param name="method" value="laplace"/>
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48 <conditional name="log">
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49 <param name="log_transform" value="no"/>
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50 </conditional>
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51 <output name="results-relative_expression" md5="193000abf357cb14f70273ba6cd5f095"/>
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52 <output name="results-smoothed_dna" md5="3767aa13988a4dca40a07cb6970bcc60"/>
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53 <output name="results-smoothed_rna" md5="8b1bcb819c31ef0ba5ab4975582bfcf7"/>
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54 </test>
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55 <test>
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56 <param name="input_dna" value="rna_dna_norm-dna.txt"/>
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57 <param name="input_rna" value="rna_dna_norm-rna.txt"/>
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58 <param name="method" value="witten_bell"/>
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59 <conditional name="log">
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60 <param name="log_transform" value="yes"/>
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61 <param name="log_base" value="2"/>
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62 </conditional>
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63 <output name="results-relative_expression" md5="3064e6377c074c6e6e9cf7fdfd466ec9"/>
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64 <output name="results-smoothed_dna" md5="3a1203c0986d79e9cb4ac0e3a4a89f4e"/>
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65 <output name="results-smoothed_rna" md5="1038b44e52b95a867dc6341b4dd91697"/>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69 @HELP_HEADER@
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70
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71 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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72 ]]></help>
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73 <expand macro="citations"/>
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74 </tool>