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1 <tool id="make_otu_heatmap_html" name="make_otu_heatmap_html" version="1.2.1">
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2 <description>Make heatmap of OTU table</description>
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3 <requirements>
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4 <requirement type="binary">make_otu_heatmap_html.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 --galaxy_outputdir='$otu_heatmp.extra_files_path'
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9 --galaxy_datasets='^\S+\.html$:'$otu_heatmp
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10 make_otu_heatmap_html.py
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11 --otu_table_fp=$otu_table_fp
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12 --output_dir='$otu_heatmp.extra_files_path'
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13 --num_otu_hits=$num_otu_hits
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14 #if $tree != None and $tree.__str__ != 'None':
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15 --tree=$tree
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16 #end if
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17 #if $map_fname != None and $map_fname.__str__ != 'None' > 0:
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18 --map_fname=$map_fname
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19 #end if
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20 #if $sample_tree != None and $sample_tree.__str__ != 'None':
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21 --sample_tree=$sample_tree
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22 #end if
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23 $log_transform
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24 --log_eps=$log_eps
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25 </command>
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26 <inputs>
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27 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
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28 help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
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29 <param name="num_otu_hits" type="integer" value="5" label="num_otu_hits"
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30 help="This is the minimum number of Samples that an OTU is present in, for an OTU to be kept in the OTU table [default: 5]"/>
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31 <param name="tree" type="data" format="tre" optional="true" label="tree"
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32 help="Tree file to be used for sorting OTUs in the heatmap"/>
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33 <param name="map_fname" type="data" format="qiimemapping" optional="true" label="map_fname"
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34 help="Metadata mapping file to be used for sorting Samples in the heatmap"/>
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35 <param name="sample_tree" type="data" format="tre" optional="true" label="sample_tree"
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36 help="Tree file to be used for sorting samples (e.g, output from upgma_cluster.py). If both this and the sample mapping file are provided, the mapping file is ignored."/>
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37 <param name="log_transform" type="boolean" truevalue="--log_transform" falsevalue="" checked="false" label="log_transform"
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38 help="Data will be log-transformed. 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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39 <param name="log_eps" type="float" value="0.0" label="log_eps"
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40 help="Small value to replace zeros for log transform. [default: 1/2 the smallest non-zero entry]."/>
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41 </inputs>
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42 <outputs>
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43 <!-- TODO
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44 the html output has a js sub dir:
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45 move the js/* to the html .extra_files_path/
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46 filter the html to remove 'js/' sub dir
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47 -->
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48 <data name="otu_heatmp" format="html" label="${tool.name} on ${on_string}: otu_heatmp"/>
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49 </outputs>
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50 <tests>
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51 </tests>
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52 <help>For more information, see make_otu_heatmap_html_ in the Qiime documentation.
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53
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54 Updated and validated 02/10/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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55
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56 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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57
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58 .. _make_otu_heatmap_html: http://qiime.org/scripts/make_otu_heatmap_html.html</help>
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59 </tool>
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