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1 <tool id="collate_alpha" name="collate_alpha" version="1.2.0">
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2 <description>Collate alpha diversity results</description>
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3 <requirements>
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4 <requirement type="binary">collate_alpha.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=$output1.extra_files_path
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9 --galaxy_new_files_path='$__new_file_path__'
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10 --galaxy_logfile=$output1
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11 --galaxy_new_datasets='^\S+\.txt$:txt'
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12 --galaxy_datasetid=$output1.id
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13 collate_alpha.py
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14 --input_path=$input_path.extra_files_path
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15 --output_path='$__new_file_path__'
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16 </command>
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17 <inputs>
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18 <param name="input_path" type="data" format="txt" label="input_path"
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19 help="Input is alpha diversity log file [REQUIRED]"/>
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20 <!--<param name="example_path" type="text" label="example_path"
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21 help="example alpha_diversity analysis file, containing all samples and all metrics to be included in the collated result[Default: chosen automatically (see usage string)]"/>-->
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22 </inputs>
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23 <outputs>
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24 <data format="txt" name="output1" label="${tool.name} on ${on_string}"/>
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25 </outputs>
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26 <tests>
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27 </tests>
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28 <help>This tool concatenates all the files generated by alpha_diversity in order to generate rarefaction curves. The input is therefore the log file generated by alpha_diversity, and the output is a log file listing all the output files, as well as the files themselves. Galaxy must be manually refreshed after running this tool to view all output files.
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29
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30 For more information, see collate_alpha_ in the Qiime documentation.
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31
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32 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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33
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34 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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35
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36 .. _collate_alpha: http://qiime.org/scripts/collate_alpha.html</help>
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37 </tool>
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38
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