Mercurial > repos > bebatut > humann2

annotate in_development/humann2_rna_dna_norm.xml @ 5:2bf5fcf30e1f draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit e5b8f29dde45dddcda6ee283212dd1bdde487f87-dirty
author bebatut
date Fri, 18 Dec 2015 08:34:43 -0500
parents 947012405a6e
children 0d3d44f13122
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1 <tool id="humann2_rna_dna_norm" name="Combine metagenomic and metatranscriptomic HUMAnN2 data" version="0.1.0">
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2 <description></description>
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4 <requirements>
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5 <requirement type="package" version="2.2.4">bowtie2</requirement>
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6 <requirement type="package" version="2.0">metaphlan2</requirement>
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7 <requirement type="package" version="0.6.13">diamond</requirement>
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8 <requirement type="package" version="2.0">humann2</requirement>
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9 </requirements>
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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15 <version_command>
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16 <![CDATA[
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17 humann2_rna_dna_norm --version
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18 ]]>
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19 </version_command>
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21 <command><![CDATA[
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22 humann2_rna_dna_norm
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23 --input_dna $input_dna
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24 --input_rna $input_rna
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25 --output_basename "combined"
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26 $log_transform.test
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27 #if $log_transform.test:
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28 --log_base $log_transform.log_base
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29 #end if
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30 ]]></command>
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32 <inputs>
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33 <param name="input_dna" type="data" format="tsv" label="Metagenomic table"
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34 help="(--input_dna)"/>
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35 <param name="input_rna" type="data" format="tsv" label="Metatranscriptomic table"
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36 help="(--input_rna)"/>
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37
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38 <conditional name="log_transform">
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39 <param name='test' type='boolean' checked="false"
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40 truevalue='--log_transform' falsevalue=''
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41 label="Report log-transformed relative expression values?"
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42 help="(--log_transform)"/>
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43 <when value="--log_transform">
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44 <param name="log_base" type="integer" min="0" max="10" value="2"
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45 label="Base for log transformation" help="(--log_base)"/>
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46 </when>
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47 <when value=""/>
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48 </conditional>
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49 </inputs>
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50
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51 <outputs>
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52 <data format="tsv" name="smoothed_dna"
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53 from_work_dir="combined"
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54 label="Smoothed DNA data for ${on_string} (HUMAnN2)" />
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55 <data format="tsv" name="smoothed_rna"
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56 from_work_dir="combined"
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57 label="Smoothed RNA data for ${on_string} (HUMAnN2)" />
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58 <data format="tsv" name="normalized_rna"
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59 from_work_dir="combined"
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60 label="Normalized RNA data for ${on_string} (HUMAnN2)" />
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61 </outputs>
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62
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63 <tests>
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64 </tests>
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65
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66 <help><![CDATA[
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67 **What it does**
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68
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69 This tool normalizes combined meta'omic sequencing data.
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70
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71 Given a DNA table and a RNA table, it produces 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 Witten-Bell smoothing procedure is used here.
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72
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73 If working with stratified data, smoothing is carried out on the stratified values and then community totals are recomputed.
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74
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75 The DNA and RNA columns must be 1:1 and in the same order. The units of the table should be count-like (for example, HUMAnN2 gene family abundance files).gene and pathway abundance tables.
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76
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77 HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
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78
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79 ]]></help>
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80
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81 <citations>
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82 </citations>
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83 </tool>