Mercurial > repos > simon-gladman > phyloseq_filter

annotate phyloseq_filter.xml @ 2:54897b7e0551 draft default tip

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Updated tool
author simon-gladman
date Thu, 22 Nov 2018 08:13:52 -0500
parents 9fbb104e16d9
children
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1 <tool id="biom_filter" name="Phyloseq Biom Filtering" version="1.22.3.2" hidden="false">
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2 <description>biom file filter</description>
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3 <requirements>
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4 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <requirement type="package" version="1.0.11">r-doparallel</requirement>
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7 <requirement type="package" version="1.20.0">bioconductor-metagenomeseq</requirement>
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8 <requirement type="package" version="9.18">ghostscript</requirement>
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9 </requirements>
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10 <version_command><![CDATA[
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11 echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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12 ]]></version_command>
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13 <command detect_errors="exit_code"><![CDATA[
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14 Rscript '${__tool_directory__}/phyloseq_filter.R'
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15 #if str($file_source.file_source_selector) == "set_biom":
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16 --biom='$file_source.input'
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17 #else:
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18 --otu_table='$OTU_TABLE'
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19 --tax_table='$TAX_TABLE'
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20 --meta_table='$META_TABLE'
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21 #end if
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22 --cutoff='$cutoff'
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23 --kingdom='$kingdom_field'
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24 --keep='$keep'
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25 --filter='$nsample'
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26 --outbiom='$outputbiom'
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27 --outdir="$htmlfile.files_path"
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28 --htmlfile='$htmlfile'
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29 ]]>
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30 </command>
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31
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32 <inputs>
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33 <conditional name="file_source">
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34 <param name="file_source_selector" type="select" label="Choose an input file type">
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35 <option value="set_biom" selected="True">BIOM File</option>
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36 <option value="set_table">TABULAR File</option>
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37 </param>
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38 <when value="set_biom">
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39 <param format="biom1" name="input" type="data" label="Input File"/>
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40 </when>
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41 <when value="set_table">
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42 <param format="tabular" name="OTU_TABLE" type="data" label="OTU table"/>
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43 <param format="tabular" name="TAX_TABLE" type="data" label="Taxonomy table"/>
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44 <param format="tabular" name="META_TABLE" type="data" label="Metadata table"/>
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45 </when>
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46 </conditional>
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47 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
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48 <option value="Kingdom">Kingdom</option>
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49 <option value="Phylum" selected="true">Phylum</option>
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50 <option value="Class">Class</option>
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51 <option value="Order">Order</option>
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52 <option value="Family">Family</option>
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53 <option value="Genus">Genus</option>
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54 <option value="Species">Species</option>
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55 </param>
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56 <param name="keep" size="10" type="integer" value="5" label="Number of the most abundant taxonomic rank units to keep in the filtered BIOM file" help="e.g. Phyla, Class and etc. as specified above. Select a value > 1."/>
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57 <param name="cutoff" size="10" type="integer" value="1" label="Filter out OTUs. Remove OTUs from the analysis that do not appear more than X times in more than Y% of the samples. Specify value of X" help="Remove OTUs that do not appear more than X times (e.g., 5 times)"/>
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58 <param name="nsample" size="10" type="float" value="0.0" label="Specify value of Y (where 1.0 = 100%)"/>
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59 </inputs>
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60
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61 <outputs>
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62 <data format="biom1" name="outputbiom" label="${tool.name} on ${on_string}.biom"/>
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63 <data format="html" name="htmlfile" label="${tool.name} on ${on_string} Sample Abundance plot.html"/>
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64 </outputs>
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65
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66 <tests>
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67 <test> <!-- Test #1: Test BIOM format input -->
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68 <conditional name="file_source">
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69 <param name="file_source_selector" value="set_biom"/>
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70 <param name="input" value="GP.biom" ftype="biom1"/>
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71 </conditional>
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72 <output name="htmlfile" ftype="html" file="biom_out.html" />
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73 <output name="outputbiom" >
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74 <assert_contents>
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75 <has_text text="Biological Observation Matrix"/>
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76 </assert_contents>
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77 </output>
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78 </test>
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79 <test> <!-- Test #2: Test TABULAR format inputs -->
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80 <conditional name="file_source">
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81 <param name="file_source_selector" value="set_table" />
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82 <param name="OTU_TABLE" value="GP_OTU_TABLE.txt" />
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83 <param name="TAX_TABLE" value="GP_TAX_TABLE.txt" />
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84 <param name="META_TABLE" value="GP_SAMPLE_TABLE.txt" />
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85 </conditional>
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86 <output name="htmlfile" ftype="html" file="matrix_out.html" />
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87 <output name="outputbiom" >
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88 <assert_contents>
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89 <has_text text="Biological Observation Matrix"/>
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90 </assert_contents>
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91 </output>
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92 </test>
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93 </tests>
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94
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95 <help>
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96 **What it does**
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97 Filter out low abundance OTUs and/or data corresponding to the least represented taxonomic grouping using R package called R_package_called_phyloseq_, and specifically according to the pre-processing step outlined in the Phyloseq_Ordination_Plot_Tutorial_.
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98
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99 .. _R_package_called_phyloseq: https://joey711.github.io/phyloseq/index.html
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100 .. _Phyloseq_Ordination_Plot_Tutorial: https://joey711.github.io/phyloseq/plot_ordination-examples.html
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101
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102 -----
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103
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104 **Input**
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105
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106 - **Choose an input file type** - either 1 BIOM file or 3 TABULAR files (i.e. OTU, Taxonomy and Metadata tables)
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107 - **Select a taxonomic rank for the analysis** - if filtering out low abundance taxa, this is the level of the taxonomy that you want to filter on (e.g. phyla, species)
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108 - **Number of the most abundant taxonomic rank units to keep in the filtered BIOM file** - the number of the most abundant taxonomic rank units specified above to keep (e.g. remove all the most abundant 5 phyla or species)
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109 - **Specify value of X** - if filtering out low abundance OTUs, use this to specify a value of X (where OTUs are removed that do not appear more than X times in more than Y% of the samples)
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110 - **Specify value of Y (where 1.0=100%)** - if filtering out low abundance OTUs use this to specify a value of Y (where OTUs are removed that do not appear more than X times in more than Y% of the samples)
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111
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112 -----
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113
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114 =========
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115 Resources
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116 =========
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117
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118 **Wrapper Authors**
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119
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120 QFAB Bioinformatics (support@qfab.org)
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121 Melbourne Bioinformatics
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122 </help>
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123 <citations>
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124 <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
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125 </citations>
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126 </tool>