Mercurial > repos > jjohnson > qiime
comparison make_otu_heatmap_html.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
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| date | Sun, 17 Jul 2011 10:30:11 -0500 |
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| -1:000000000000 | 0:e5c3175506b7 |
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| 1 <tool id="make_otu_heatmap_html" name="make_otu_heatmap_html" version="1.2.1"> | |
| 2 <description>Make heatmap of OTU table</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">make_otu_heatmap_html.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_outputdir='$otu_heatmp.extra_files_path' | |
| 9 --galaxy_datasets='^\S+\.html$:'$otu_heatmp | |
| 10 make_otu_heatmap_html.py | |
| 11 --otu_table_fp=$otu_table_fp | |
| 12 --output_dir='$otu_heatmp.extra_files_path' | |
| 13 --num_otu_hits=$num_otu_hits | |
| 14 #if $tree != None and $tree.__str__ != 'None': | |
| 15 --tree=$tree | |
| 16 #end if | |
| 17 #if $map_fname != None and $map_fname.__str__ != 'None' > 0: | |
| 18 --map_fname=$map_fname | |
| 19 #end if | |
| 20 #if $sample_tree != None and $sample_tree.__str__ != 'None': | |
| 21 --sample_tree=$sample_tree | |
| 22 #end if | |
| 23 $log_transform | |
| 24 --log_eps=$log_eps | |
| 25 </command> | |
| 26 <inputs> | |
| 27 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp" | |
| 28 help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/> | |
| 29 <param name="num_otu_hits" type="integer" value="5" label="num_otu_hits" | |
| 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]"/> | |
| 31 <param name="tree" type="data" format="tre" optional="true" label="tree" | |
| 32 help="Tree file to be used for sorting OTUs in the heatmap"/> | |
| 33 <param name="map_fname" type="data" format="qiimemapping" optional="true" label="map_fname" | |
| 34 help="Metadata mapping file to be used for sorting Samples in the heatmap"/> | |
| 35 <param name="sample_tree" type="data" format="tre" optional="true" label="sample_tree" | |
| 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."/> | |
| 37 <param name="log_transform" type="boolean" truevalue="--log_transform" falsevalue="" checked="false" label="log_transform" | |
| 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."/> | |
| 39 <param name="log_eps" type="float" value="0.0" label="log_eps" | |
| 40 help="Small value to replace zeros for log transform. [default: 1/2 the smallest non-zero entry]."/> | |
| 41 </inputs> | |
| 42 <outputs> | |
| 43 <!-- TODO | |
| 44 the html output has a js sub dir: | |
| 45 move the js/* to the html .extra_files_path/ | |
| 46 filter the html to remove 'js/' sub dir | |
| 47 --> | |
| 48 <data name="otu_heatmp" format="html" label="${tool.name} on ${on_string}: otu_heatmp"/> | |
| 49 </outputs> | |
| 50 <tests> | |
| 51 </tests> | |
| 52 <help> | |
| 53 | |
| 54 | |
| 55 </help> | |
| 56 </tool> | |
| 57 |