Mercurial > repos > simon-gladman > phyloseq_nmds
annotate phyloseq_nmds.xml @ 2:20adf95eb758 draft
Updated phyloseq_nmds.xml to allow for new datatype.
| author | simon-gladman |
|---|---|
| date | Fri, 20 Jul 2018 00:23:53 -0400 |
| parents | b4606394e7ec |
| children | 5a2bda9b28c5 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="phyloseq_nmds" name="Phyloseq NMDS" version="1.22.3.1" hidden="false"> |
| 2 <description>Phyloseq NMDS plot</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement> | |
| 5 <requirement type="package" version="1.20.0">r-getopt</requirement> | |
| 6 <requirement type="package" version="9.18">ghostscript</requirement> | |
| 7 </requirements> | |
| 8 <version_command><![CDATA[ | |
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9 echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ") |
| 0 | 10 ]]></version_command> |
| 11 <command detect_errors="exit_code"><![CDATA[ | |
| 12 Rscript '${__tool_directory__}/phyloseq_nmds.R' | |
| 13 #if str($file_source.file_source_selector) == "set_biom": | |
| 14 --biom='$file_source.input' | |
| 15 --subset='$file_source.subsetColumn' | |
| 16 #else: | |
| 17 --otu_table='$OTU_TABLE' | |
| 18 --tax_table='$TAX_TABLE' | |
| 19 --meta_table='$META_TABLE' | |
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20 --category='$file_source.category' |
| 0 | 21 #end if |
| 22 --method='$ord_method' | |
| 23 --distance='$distance' | |
| 24 --kingdom='$kingdom_field' | |
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25 --cutoff='$cutoff' |
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26 --keep='$keep' |
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27 --filter='$nsample' |
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28 --plottype='$plot_type' |
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29 --outdir="$htmlfile.files_path" |
| 0 | 30 --htmlfile='$htmlfile' |
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31 ]]> |
| 0 | 32 </command> |
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33 |
| 0 | 34 <inputs> |
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35 |
| 0 | 36 <conditional name="file_source"> |
| 37 <param name="file_source_selector" type="select" label="Choose a file type"> | |
| 38 <option value="set_biom" selected="True">BIOM File</option> | |
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39 <option value="set_table">TABULAR File</option> |
| 0 | 40 </param> |
| 41 <when value="set_biom"> | |
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42 <param format="biom1" name="input" type="data" label="Input File"/> |
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43 <!--<param format="tabular" name="META_COLUMN" type="data" label="Column File"/>--> |
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44 <param name="subsetColumn" type="select" label="Select a column"> |
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45 <options> |
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46 <filter type="data_meta" ref="input" key="table_column_metadata_headers" /> |
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47 </options> |
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48 </param> |
| 0 | 49 </when> |
| 50 <when value="set_table"> | |
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51 <param format="tabular" name="OTU_TABLE" type="data" label="OTU table"/> |
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52 <param format="tabular" name="TAX_TABLE" type="data" label="Taxonomy table"/> |
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53 <param format="tabular" name="META_TABLE" type="data" label="Metadata table"/> |
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54 <param name="category" type="data_column" data_ref="META_TABLE" use_header_names="True" label="Select a column"/> |
| 0 | 55 </when> |
| 56 </conditional> | |
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57 <param name="plot_type" type="select" label="Type of Plot" help="NMDS plot by type (e.g., OTU, SAMPLE)"> |
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58 <option value="1">OTU</option> |
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59 <option value="2">SAMPLE</option> |
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60 </param> |
| 0 | 61 <param name="ord_method" type="select" display="radio" label="Select NMDS method"> |
| 62 <option value="NMDS" selected="true">NMDS</option> | |
| 63 <option value="DCA">DCA</option> | |
| 64 <option value="CCA">CCA</option> | |
| 65 <option value="RDA">RDA</option> | |
| 66 <option value="DPCoA">DPCoA</option> | |
| 67 <option value="MDS">MDS</option> | |
| 68 <option value="PCoA">PCoA</option> | |
| 69 </param> | |
| 70 <param name="distance" type="select" display="radio" label="Select a distance for NMDS"> | |
| 71 <option value="bray" selected="true">bray</option> | |
| 72 <option value="gower">gower</option> | |
| 73 <option value="unifrac">unifrac</option> | |
| 74 </param> | |
| 75 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomy rank"> | |
| 76 <option value="Kingdom">Kingdom</option> | |
| 77 <option value="Phylum" selected="true">Phylum</option> | |
| 78 <option value="Class">Class</option> | |
| 79 <option value="Order">Order</option> | |
| 80 <option value="Family">Family</option> | |
| 81 <option value="Genus">Genus</option> | |
| 82 <option value="Species">Species</option> | |
| 83 </param> | |
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84 <param name="nsample" size="10" type="float" value="0.5" label="Number of samples to keep" help="The percentage of sample number to keep for analysis (e.g., 0.5 is equivalent to half of the samples to keep for analysis)"/> |
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85 <param name="cutoff" size="10" type="integer" value="5" label="Cutoff value for filtering OTU table" help="Remove OTUs that do not appear more than 5 times"/> |
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86 <param name="keep" size="10" type="integer" value="5" label="Number of most abundant phyla" help="provide the number of most abundancet phyla to display"/> |
| 0 | 87 </inputs> |
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88 |
| 0 | 89 <outputs> |
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90 <data format="html" name="htmlfile" label="${tool.name}.html"/> |
| 0 | 91 </outputs> |
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92 |
| 0 | 93 <tests> |
| 94 <test> <!-- Test #1: Test BIOM format input --> | |
| 95 <!-- Equivalent command (replace + with double dash): Rscript phyloseq_nmds.R +biom=test-data/GP.biom +subset=6 +method=NMDS | |
| 96 +distance=bray +kingdom=Phylum +cutoff=5 +keep=5 +outdir=outputdir +htmlfile=biom_out.html --> | |
| 97 <conditional name="file_source"> | |
| 98 <param name="file_source_selector" value="set_biom"/> | |
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99 <param name="input" value="GP.biom" format="biom1"/> |
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100 <param name="subsetColumn" value="Primer" /> |
| 0 | 101 </conditional> |
| 102 <output name="htmlfile" ftype="html" file="biom_out.html" /> | |
| 103 </test> | |
| 104 <test><!-- Test #2: Test TABULAR format inputs --> | |
| 105 <!-- Equivalent command (replace + with double dash): Rscript phyloseq_nmds.R +otu_table=test-data/GP_OTU_TABLE.txt | |
| 106 +tax_table=test-data/GP_TAX_TABLE.txt +meta_table=test-data/GP_SAMPLE_TABLE.txt | |
| 107 +method="bray" +kingdom=Phylum +cutoff=5 + keep=5 +category=6 +outdir=outputdir +htmlfile=test.html --> | |
| 108 <conditional name="file_source"> | |
| 109 <param name="file_source_selector" value="set_table" /> | |
| 110 <param name="OTU_TABLE" value="GP_OTU_TABLE.txt" /> | |
| 111 <param name="TAX_TABLE" value="GP_TAX_TABLE.txt" /> | |
| 112 <param name="META_TABLE" value="GP_SAMPLE_TABLE.txt" /> | |
| 113 <param name="category" value="6" /> | |
| 114 </conditional> | |
| 115 <output name="htmlfile" ftype="html" file="test.html" /> | |
| 116 </test> | |
| 117 </tests> | |
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118 |
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119 <help> |
| 0 | 120 **What it does** |
| 121 Creates NMDS plot using R package called phyloseq_. | |
| 122 | |
| 123 .. _phyloseq: https://joey711.github.io/phyloseq/plot_ordination-examples.html | |
| 124 | |
| 125 ----- | |
| 126 | |
| 127 **Input** | |
| 128 | |
| 129 - **Choose a file type** - BIOM File or TABULAR file | |
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130 - **Select a column** - This column is used to extract unique value from the column of interest for NMDS plot |
| 0 | 131 - **OTU TABLE** - this is a OTU matrix |
| 132 - **Taxonomy TABLE** - this is a TAX matrix | |
| 133 - **Metadata TABLE** - this is a metadata file of the experiment design | |
| 134 - **Select NMDS method** - select a method for NMDS plot | |
| 135 - **Select a distance for NMDS** - select a distance option for NMDS plot | |
| 136 - **Select a taxonomy rank** - select a taxonomy for NMDS plot | |
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137 - **Number of samples to keep** - Number of samples to keep for analysis |
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138 - **Cutoff value for filtering OTU table** - this cutoff value is used to fitler OTU table |
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139 - **Number of most abundant phyla** - a number of most abundant phyla to be display in NMDS plot |
| 0 | 140 </help> |
| 141 <citations> | |
| 142 <citation type="doi">10.18129/B9.bioc.phyloseq</citation> | |
| 143 </citations> | |
| 144 </tool> |