Mercurial > repos > iuc > qiime_make_otu_heatmap

annotate make_otu_heatmap.xml @ 6:a3b69e0b9246 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 19:54:15 -0400
parents 06cb29d26718
children dd5418b9a32c
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a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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1 <tool id="qiime_make_otu_heatmap" name="Plot heatmap of OTU table" version="@WRAPPER_VERSION@.0">
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2 <description>(make_otu_heatmap)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>make_otu_heatmap.py --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 make_otu_heatmap.py
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10 --otu_table_fp '$otu_table_fp'
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11
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12 #if $imagetype == "pdf"
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13 --output_fp '$pdf_output_fp'
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14 #else if $imagetype == "png"
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15 --output_fp '$png_output_fp'
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16 #else if $imagetype == "svg"
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17 --output_fp '$svg_output_fp'
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18 #end if
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19
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20 #if $otu_tree
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21 --otu_tree '$otu_tree'
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22 #end if
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23 #if $map_fname
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24 --map_fname '$map_fname'
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25 #end if
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26 #if str($category) != ''
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27 --category '$category'
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28 #end if
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29 #if $sample_tree
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30 --sample_tree '$sample_tree'
06cb29d26718 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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31 #end if
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32 --imagetype '$imagetype'
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33 $no_log_transform
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34 $suppress_row_clustering
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35 $suppress_column_clustering
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36 $absolute_abundance
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37
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38 #if str($ad.select) == "yes":
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39 --color_scheme '$ad.color_scheme'
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40 --width '$ad.width'
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41 --height '$ad.height'
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42 --dpi '$ad.dpi'
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43 --obs_md_category '$ad.obs_md_category'
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44 #if str($ad.obs_md_level) != ''
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45 --obs_md_level '$ad.obs_md_level'
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46 #end if
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47 #end if
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48 ]]></command>
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49 <inputs>
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50 <param argument="--otu_table_fp" type="data" format="biom1" label="Input OTU table"/>
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51 <param argument="--otu_tree" type="data" format="txt" optional="true" label="Tree file to be used for sorting OTUs in the heatmap"/>
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52 <param argument="--map_fname" type="data" format="txt" optional="true" label="Metadata mapping file to be used for sorting"/>
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53 <param argument="--category" type="text" optional="True" label="Metadata category for sorting samples" help=" Samples will be clustered within each category level using euclidean UPGMA"/>
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54 <param argument="--sample_tree" type="data" format="txt" optional="true" label="Tree file to be used for sorting samples" help="If both this and the sample mapping file are provided, the mapping file is ignored."/>
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55 <param argument="--imagetype" type="select" label="Type of image to produce">
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56 <option value="pdf" selected="true">PDF</option>
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57 <option value="png">PNG</option>
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58 <option value="svg">SVG</option>
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59 </param>
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60 <param argument="--no_log_transform" type="boolean" truevalue="--no_log_transform" falsevalue="" checked="false" label="Data will not be log-transformed the data?" help="Without this option, all zeros will be set to a small value (default is 1/2 the smallest non-zero entry). Data will be translated to be non-negative after log transform, and num_otu_hits will be set to 0."/>
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61 <param argument="--suppress_row_clustering" type="boolean" truevalue="--suppress_row_clustering" falsevalue="" checked="false" label="Perform no UPGMA clustering of OTUs (rows)?" help="If --otu_tree is provided, this flag is ignored."/>
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62 <param argument="--suppress_column_clustering" type="boolean" truevalue="--suppress_column_clustering" falsevalue="" checked="false" label="Perform no UPGMA clustering of Samples (columns)?" help="If --map_fname is provided, this flag is ignored."/>
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63 <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="Do not normalize samples to sum to 1?"/>
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64 <conditional name="ad">
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65 <param name="select" type="select" label="Show advanced options">
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66 <option value="no" selected="true">No</option>
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67 <option value="yes">Yes</option>
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68 </param>
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69 <when value="no"/>
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70 <when value="yes">
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71 <param argument="--color_scheme" type="select" label="Color scheme for figure" help="More details in http://matplotlib.org/examples/color/colormaps_reference.html">
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72 <option value="viridis">viridis (Perceptually Uniform Sequential)</option>
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73 <option value="inferno">inferno (Perceptually Uniform Sequential)</option>
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74 <option value="plasma">plasma (Perceptually Uniform Sequential)</option>
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75 <option value="magma">magma (Perceptually Uniform Sequential)</option>
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76 <option value="Blues">Blues (Sequential)</option>
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77 <option value="BuGn">BuGn (Sequential)</option>
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78 <option value="BuPu">BuPu (Sequential)</option>
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79 <option value="GnBu">GnBu (Sequential)</option>
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80 <option value="Greens">Greens (Sequential)</option>
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81 <option value="Greys">Greys (Sequential)</option>
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82 <option value="Oranges">Oranges (Sequential)</option>
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83 <option value="OrRd">OrRd (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
84 <option value="PuBu">PuBu (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
85 <option value="PuBuGn">PuBuGn (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
86 <option value="PuRd">PuRd (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
87 <option value="Purples">Purples (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
88 <option value="RdPu">RdPu (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
89 <option value="Reds">Reds (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
90 <option value="YlGn" selected="true">YlGn (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
91 <option value="YlGnBu">YlGnBu (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
92 <option value="YlOrBr">YlOrBr (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
93 <option value="YlOrRd">YlOrRd (Sequential)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
94 <option value="afmhot">afmhot (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
95 <option value="autumn">autumn (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
96 <option value="bone">bone (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
97 <option value="cool">cool (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
98 <option value="copper">copper (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
99 <option value="gist_heat">gist_heat (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
100 <option value="gray">gray (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
101 <option value="hot">hot (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
102 <option value="pink">pink (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
103 <option value="spring">spring (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
104 <option value="summer">summer (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
105 <option value="winter">winter (Sequential (2))</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
106 <option value="BrBG">BrBG (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
107 <option value="bwr">bwr (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
108 <option value="coolwarm">coolwarm (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
109 <option value="PiYG">PiYG (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
110 <option value="PRGn">PRGn (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
111 <option value="PuOr">PuOr (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
112 <option value="RdBu">RdBu (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
113 <option value="RdGy">RdGy (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
114 <option value="RdYlBu">RdYlBu (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
115 <option value="RdYlGn">RdYlGn (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
116 <option value="Spectral">Spectral (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
117 <option value="seismic">seismic (Diverging)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
118 <option value="Accent">Accent (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
119 <option value="Dark2">Dark2 (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
120 <option value="Paired">Paired (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
121 <option value="Pastel1">Pastel1 (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
122 <option value="Pastel2">Pastel2 (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
123 <option value="Set1">Set1 (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
124 <option value="Set2">Set2 (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
125 <option value="Set3">Set3 (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
126 <option value="Vega10">Vega10 (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
127 <option value="Vega20">Vega20 (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
128 <option value="Vega20b">Vega20b (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
129 <option value="Vega20c">Vega20c (Qualitative)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
130 <option value="gist_earth">gist_earth (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
131 <option value="terrain">terrain (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
132 <option value="ocean">ocean (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
133 <option value="gist_stern">gist_stern (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
134 <option value="brg">brg (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
135 <option value="CMRmap">CMRmap (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
136 <option value="cubehelix">cubehelix (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
137 <option value="gnuplot">gnuplot (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
138 <option value="gnuplot2">gnuplot2 (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
139 <option value="gist_ncar">gist_ncar (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
140 <option value="nipy_spectral">nipy_spectral (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
141 <option value="jet">jet (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
142 <option value="rainbow">rainbow (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
143 <option value="gist_rainbow">gist_rainbow (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
144 <option value="hsv">hsv (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
145 <option value="flag">flag (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
146 <option value="prism">prism (Miscellaneous)</option>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
147 </param>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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148 <param argument="--width" type="float" value="5" label="Width of the figure in inches"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
149 <param argument="--height" type="float" value="5" label="Height of the figure in inches"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
150 <param argument="--dpi" type="integer" value="" label="Resolution of the figure in dots per inch"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
151 <param argument="--obs_md_category" type="text" value="taxonomy" label="Observation metadata category to plot"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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diff changeset
152 <param argument="--obs_md_level" type="text" value="" label="The level of observation metadata to plot for hierarchical metadata" optional="true"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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153 </when>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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154 </conditional>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
155 </inputs>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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156 <outputs>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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157 <data name="pdf_output_fp" format="pdf" label="${tool.name} on ${on_string}: OTU Heatmap">
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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158 <filter>imagetype == 'pdf'</filter>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
159 </data>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
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160 <data name="png_output_fp" format="png" label="${tool.name} on ${on_string}: OTU Heatmap">
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
161 <filter>imagetype == 'png'</filter>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
parents:
diff changeset
162 </data>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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163 <data name="svg_output_fp" format="svg" label="${tool.name} on ${on_string}: OTU Heatmap">
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
iuc
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164 <filter>imagetype == 'svg'</filter>
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165 </data>
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166 </outputs>
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167 <tests>
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168 <test>
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169 <param name="otu_table_fp" value="make_otu_heatmap/otu_table.biom"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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170 <param name="imagetype" value="pdf"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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171 <param name="no_log_transform" value=""/>
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172 <param name="suppress_row_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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173 <param name="suppress_column_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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174 <param name="absolute_abundance" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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175 <param name="select" value="yes"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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176 <param name="color_scheme" value="YlGn"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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diff changeset
177 <param name="width" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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178 <param name="height" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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179 <param name="dpi" value="200"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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180 <param name="obs_md_category" value="taxonomy"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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181 <output name="pdf_output_fp" file="make_otu_heatmap/basic_heatmap.pdf" compare="sim_size" />
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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182 </test>
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183 <test>
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184 <param name="otu_table_fp" value="make_otu_heatmap/otu_table.biom"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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185 <param name="imagetype" value="png"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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186 <param name="no_log_transform" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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187 <param name="suppress_row_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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188 <param name="suppress_column_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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189 <param name="absolute_abundance" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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190 <param name="select" value="yes"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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191 <param name="color_scheme" value="YlGn"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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192 <param name="width" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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193 <param name="height" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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194 <param name="dpi" value="200"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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195 <param name="obs_md_category" value="taxonomy"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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196 <output name="png_output_fp" file="make_otu_heatmap/basic_heatmap.png" compare="sim_size" />
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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197 </test>
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198 <test>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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199 <param name="otu_table_fp" value="make_otu_heatmap/otu_table.biom"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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200 <param name="imagetype" value="svg"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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diff changeset
201 <param name="no_log_transform" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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202 <param name="suppress_row_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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203 <param name="suppress_column_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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204 <param name="absolute_abundance" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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205 <param name="select" value="yes"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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206 <param name="color_scheme" value="YlGn"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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diff changeset
207 <param name="width" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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208 <param name="height" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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209 <param name="dpi" value="200"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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210 <param name="obs_md_category" value="taxonomy"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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211 <output name="svg_output_fp" file="make_otu_heatmap/basic_heatmap.svg" compare="sim_size" />
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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212 </test>
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213 <test>
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214 <param name="otu_table_fp" value="make_otu_heatmap/otu_table.biom"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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215 <param name="map_fname" value="make_otu_heatmap/mapping_file.txt"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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216 <param name="imagetype" value="pdf"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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217 <param name="no_log_transform" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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218 <param name="suppress_row_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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219 <param name="suppress_column_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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220 <param name="absolute_abundance" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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221 <param name="select" value="yes"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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222 <param name="color_scheme" value="YlGn"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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223 <param name="width" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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224 <param name="height" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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225 <param name="dpi" value="200"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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226 <param name="obs_md_category" value="taxonomy"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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227 <output name="pdf_output_fp" value="make_otu_heatmap/sample_sorted_heatmap.pdf" compare="sim_size" />
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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228 </test>
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229 <test>
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230 <param name="otu_table_fp" value="make_otu_heatmap/otu_table.biom"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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231 <param name="map_fname" value="make_otu_heatmap/mapping_file.txt"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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232 <param name="otu_tree" value="make_otu_heatmap/rep_set.tre"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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233 <param name="imagetype" value="pdf"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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234 <param name="no_log_transform" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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235 <param name="suppress_row_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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236 <param name="suppress_column_clustering" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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237 <param name="absolute_abundance" value=""/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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238 <param name="select" value="yes"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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239 <param name="color_scheme" value="YlGn"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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240 <param name="width" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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241 <param name="height" value="5"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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242 <param name="dpi" value="200"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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243 <param name="obs_md_category" value="taxonomy"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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244 <output name="pdf_output_fp" value="make_otu_heatmap/sample_otu_sorted_heatmap.pdf" compare="sim_size" />
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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245 </test>
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246 <test>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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247 <param name="otu_table_fp" value="make_otu_heatmap/otu_table.biom"/>
a3d1104d090c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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248 <param name="map_fname" value="make_otu_heatmap/mapping_file.txt"/>
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249 <param name="category" value="Treatment"/>
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250 <param name="imagetype" value="pdf"/>
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251 <param name="no_log_transform" value=""/>
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252 <param name="suppress_row_clustering" value=""/>
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253 <param name="suppress_column_clustering" value=""/>
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254 <param name="absolute_abundance" value=""/>
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255 <param name="select" value="yes"/>
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256 <param name="color_scheme" value="YlGn"/>
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257 <param name="width" value="5"/>
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258 <param name="height" value="5"/>
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259 <param name="dpi" value="200"/>
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260 <param name="obs_md_category" value="taxonomy"/>
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261 <output name="pdf_output_fp" value="make_otu_heatmap/treatment_sample_sorted_heatmap.pdf" compare="sim_size" />
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262 </test>
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263 </tests>
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264 <help><![CDATA[
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265 **What it does**
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266
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267 This script visualizes an OTU table as a heatmap where each row corresponds to an OTU and each column corresponds to a sample. The higher the relative abundance of an OTU in a sample, the more intense the color at the corresponsing position in the heatmap. By default, the OTUs (rows) will be clustered by UPGMA hierarchical clustering, and the samples (columns) will be presented in the order in which they appear in the OTU table. Alternatively, the user may supply a tree to sort the OTUs (rows) or samples (columns), or both. The user may also pass in a mapping file for sorting samples. If the user passes in a mapping file and a metadata category, samples (columns) will be grouped by category value and subsequently clustered within each group.
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268
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269 A single output file is created containing the heatmap of the OTU table (a PDF file by default).
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270 ]]></help>
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271 <citations>
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272 <expand macro="citations"/>
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273 </citations>
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274 </tool>