Mercurial > repos > simon-gladman > phyloseq_nmds
annotate phyloseq_nmds.xml @ 4:d06ddf67468f draft default tip
planemo upload commit 5ca7dbbc2e9d6107b706376cd36742cf0c816534-dirty
| author | simon-gladman |
|---|---|
| date | Tue, 04 Sep 2018 21:41:23 -0400 |
| parents | 5a2bda9b28c5 |
| children |
| rev | line source |
|---|---|
| 3 | 1 <tool id="phyloseq_nmds" name="Phyloseq Ordination Plot" version="1.22.3.2" hidden="false"> |
| 2 <description>Ordination Plotting</description> | |
| 0 | 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[ | |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
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' | |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
20 --category='$file_source.category' |
| 0 | 21 #end if |
| 22 --method='$ord_method' | |
| 23 --distance='$distance' | |
| 24 --kingdom='$kingdom_field' | |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
25 --cutoff='$cutoff' |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
26 --keep='$keep' |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
27 --filter='$nsample' |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
28 --plottype='$plot_type' |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
29 --outdir="$htmlfile.files_path" |
| 0 | 30 --htmlfile='$htmlfile' |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
31 ]]> |
| 0 | 32 </command> |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
33 |
| 0 | 34 <inputs> |
| 35 <conditional name="file_source"> | |
| 3 | 36 <param name="file_source_selector" type="select" label="Choose an input file type"> |
| 0 | 37 <option value="set_biom" selected="True">BIOM File</option> |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
38 <option value="set_table">TABULAR File</option> |
| 0 | 39 </param> |
| 40 <when value="set_biom"> | |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
41 <param format="biom1" name="input" type="data" label="Input File"/> |
| 3 | 42 <param name="subsetColumn" type="select" label="Select variable for ordination"> |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
43 <options> |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
44 <filter type="data_meta" ref="input" key="table_column_metadata_headers" /> |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
45 </options> |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
46 </param> |
| 0 | 47 </when> |
| 48 <when value="set_table"> | |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
49 <param format="tabular" name="OTU_TABLE" type="data" label="OTU table"/> |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
50 <param format="tabular" name="TAX_TABLE" type="data" label="Taxonomy table"/> |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
51 <param format="tabular" name="META_TABLE" type="data" label="Metadata table"/> |
| 3 | 52 <param name="category" type="data_column" data_ref="META_TABLE" use_header_names="True" label="Select variable for ordination"/> |
| 0 | 53 </when> |
| 54 </conditional> | |
| 3 | 55 <param name="ord_method" type="select" display="radio" label="Select Ordination method"> |
| 56 <option value="NMDS" selected="true">NMDS(Non-metric Multidimensional Scalling)</option> | |
| 57 <option value="DCA">DCA (Detrended Correspondence Analysis)</option> | |
| 58 <option value="CCA">CCA (Constrained Correspondence Analysis)</option> | |
| 59 <option value="RDA">RDA (Redundancy Analysis)</option> | |
| 60 <option value="DPCoA">DPCoA (Double Principle Coordinate Analysis)</option> | |
| 61 <option value="MDS">MDS (Multidimensional Scaling)</option> | |
| 62 <option value="PCoA">PCoA (Principal Coordinate Analysis)</option> | |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
63 </param> |
| 3 | 64 <param name="distance" type="select" display="radio" label="Select Distance method"> |
| 65 <option value="bray" selected="true">bray (Bray-Curtis distance)</option> | |
| 66 <option value="gower">gower (Gower's distance)</option> | |
| 67 <option value="jsd">jds (Jensen-Shannon Divergence)</option> | |
| 68 <option value="unifrac">unifrac (unweighted UniFrac distance)</option> | |
| 69 <option value="wunifrac">wunifrac (weighted-UniFrac distance)</option> | |
| 0 | 70 </param> |
| 3 | 71 <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis"> |
| 0 | 72 <option value="Kingdom">Kingdom</option> |
| 73 <option value="Phylum" selected="true">Phylum</option> | |
| 74 <option value="Class">Class</option> | |
| 75 <option value="Order">Order</option> | |
| 76 <option value="Family">Family</option> | |
| 77 <option value="Genus">Genus</option> | |
| 78 <option value="Species">Species</option> | |
| 79 </param> | |
| 3 | 80 <param name="plot_type" type="select" label="Type of Plot" help="Ordination plot type (Plot OTUs, Plot SAMPLE, Biplot graphic, Split plot graphic)"> |
| 81 <option value="1">OTU</option> | |
| 82 <option value="2">SAMPLE</option> | |
| 83 </param> | |
| 84 <param name="nsample" size="10" type="float" value="0.5" label="Specify the number of samples to discard" help="i.e. remove OTUs from the analysis that do not appear more than X times in more than Y% of the samples (where 1.0 = 100%)"/> | |
| 85 <param name="cutoff" size="10" type="integer" value="5" label="specify value of X" help="Remove OTUs that do not appear more than X times (e.g., 5 times)"/> | |
| 86 <param name="keep" size="10" type="integer" value="5" label="Number of the most abundant taxonomic rank units to keep" help="e.g. Phyla, Class and etc"/> | |
| 0 | 87 </inputs> |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
88 |
| 0 | 89 <outputs> |
| 3 | 90 <data format="html" name="htmlfile" label="${tool.name} - ${ord_method.value_label}_${distance.value_label}.html"/> |
| 0 | 91 </outputs> |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
92 |
| 0 | 93 <tests> |
| 3 | 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 --> | |
| 0 | 97 <conditional name="file_source"> |
| 98 <param name="file_source_selector" value="set_biom"/> | |
|
4
d06ddf67468f
planemo upload commit 5ca7dbbc2e9d6107b706376cd36742cf0c816534-dirty
simon-gladman
parents:
3
diff
changeset
|
99 <param name="input" value="GP.biom" ftype="biom1" /> |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
100 <param name="subsetColumn" value="Primer" /> |
| 0 | 101 </conditional> |
| 102 <output name="htmlfile" ftype="html" file="biom_out.html" /> | |
| 103 </test> | |
| 3 | 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 --> | |
| 0 | 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> | |
|
2
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
118 |
|
20adf95eb758
Updated phyloseq_nmds.xml to allow for new datatype.
simon-gladman
parents:
0
diff
changeset
|
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 | |
| 3 | 129 - **Choose an input file type** - BIOM File or TABULAR file |
| 130 - **Select variable for ordination** - This column is used to extract unique value from the column of interest for ordination 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 | |
| 3 | 134 - **Select Ordination method** - select ordination method |
| 135 - **Select Distance method** - select distance method for ordination plot | |
| 136 - **Select a taxonomic rank for the analysis** - select a taxonomy for NMDS plot | |
| 137 - **Specify the number of samples to discard** - Y% of samples to discard (where 1.0 = 100%) | |
| 138 - **specify value of X** - Remove OTUs that do not appear more than X times (e.g., 5 times) | |
| 139 - **Number of the most abundant taxonomic rank units** - taxonomic rank units (e.g. Phyla, Class etc) to keep | |
| 140 | |
| 141 ----- | |
| 142 | |
| 143 ========= | |
| 144 Resources | |
| 145 ========= | |
| 146 | |
| 147 **Wrapper Authors** | |
| 148 | |
| 149 QFAB Bioinformatics (support@qfab.org) | |
| 150 Melbourne Bioinformatics | |
| 0 | 151 </help> |
| 152 <citations> | |
| 153 <citation type="doi">10.18129/B9.bioc.phyloseq</citation> | |
| 154 </citations> | |
| 155 </tool> |