Mercurial > repos > bebatut > compare_humann2_output

annotate compare_humann2_output.xml @ 0:9959fa526f1a draft

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author bebatut
date Wed, 20 Apr 2016 08:30:08 -0400
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1 <tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.1.0">
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2 <description>and extract information</description>
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4 <requirements>
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5 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 </stdio>
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12 <version_command></version_command>
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14 <command><![CDATA[
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15 mkdir specifics
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16 &&
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18 python $__tool_directory__/compare_humann2_output.py
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19 #for $sample in $samples:
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20 --sample_name "${sample.sample_name}"
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21 --charact_input_file "${sample.input}"
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22 --specific_output_file "specifics/specific_to_${sample.sample_name}.txt"
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23 #end for
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25 --most_abundant_characteristics_to_extract $charact_nb
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26 --more_abundant_output_file $more_abundant_output_file
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27 --similar_output_file $similar_output_file
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28 > $log
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29
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30 ]]></command>
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32 <inputs>
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33 <repeat name="samples" title="Add sample and input file (HUMAnN2 output after normalization)" >
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34 <param name="sample_name" type="text" label="Name of the sample" help="(--sample_name)"/>
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35 <param name="input" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization, --charact_input_file)"/>
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36 </repeat>
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37
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38 <param name="charact_nb" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample" help="(--most_abundant_characteristics_to_extract)"/>
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39 </inputs>
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41 <outputs>
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42 <data name="more_abundant_output_file" format="tabular"
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43 label="${tool.name} on ${on_string}: More abundant characteristics for each sample" />
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44 <data name="similar_output_file" format="tabular"
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45 label="${tool.name} on ${on_string}: Similar characteristics and the relative abundances for all samples" />
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46 <data name="log" format="txt"
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47 label="${tool.name} on ${on_string}: Log" />
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48 <collection name="specific_files" type="list">
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49 <discover_datasets pattern="__designation_and_ext__" directory="specifics"/>
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50 </collection>
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51
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52 </outputs>
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53
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54 <tests>
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55 <test>
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56 <param name="samples_0|sample_name" value="sample1"/>
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57 <param name="samples_0|input" value="humann2_m8_pathabundance_cmp_renormalized.tsv"/>
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58 <param name="samples_1|sample_name" value="sample2"/>
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59 <param name="samples_1|input" value="humann2_fasta_pathabundance_relab_renormalized.csv"/>
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60 <param name="charact_nb" value="10"/>
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61 <output name="more_abundant_output_file" file="more_abundant_output.tabular"/>
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62 <output name="similar_output_file" file="similar_output.tabular"/>
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63 <output name="log" file="log_output.txt"/>
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64 <output_collection name="specific_files" type="list">
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65 <element name="specific_to_sample1" file="specific_to_sample1_output.txt" />
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66 <element name="specific_to_sample2" file="specific_to_sample2_output.txt" />
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67 </output_collection>
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68 </test>
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69 </tests>
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70
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71 <help><![CDATA[
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72 **What it does**
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73
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74 This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted:
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75
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76 * Similar gene families or pathways between the samples and the relative abundances of these similar characteristics
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77
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78 * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples
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79
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80 * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics
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81
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82 ]]></help>
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83
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84 <citations>
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85 </citations>
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86 </tool>