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1 <tool id="make_prefs_file" name="make_prefs_file" version="2.0.0">
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2 <description>Generate preferences file</description>
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3 <requirements>
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4 <requirement type="binary">make_prefs_file.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 make_prefs_file.py
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9 --map_fname=$map_fname
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10 --output_fp=$output_fp
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11 #if $mapping_headers_to_use != None and $mapping_headers_to_use.__str__ != '':
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12 --mapping_headers_to_use=$mapping_headers_to_use
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13 #end if
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14 --background_color=$background_color
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15 --monte_carlo_dists=$monte_carlo_dists
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16 #if $input_taxa_file != None and $input_taxa_file.__str__ != '' and $input_taxa_file.__str__ != 'None':
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17 --input_taxa_file=$input_taxa_file
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18 #end if
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19 --ball_scale=$ball_scale
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20 --arrow_line_color=$arrow_line_color
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21 --arrow_head_color=$arrow_head_color
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22 </command>
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23 <inputs>
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24 <param name="map_fname" type="data" format="tabular" label="map_fname"
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25 help="This is the metadata mapping file [REQUIRED]"/>
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26 <param name="mapping_headers_to_use" type="text" label="mapping_headers_to_use"
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27 help="mapping fields to use in prefs file [default: leave empty; ALL]"/>
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28 <param name="background_color" type="text" value="black" label="background_color"
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29 help="This is the background color to use in the plots. [default: black]"/>
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30 <param name="monte_carlo_dists" type="text" value="10" label="monte_carlo_dists"
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31 help="monte carlo distanceto use for each sample header [default: 10]"/>
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32 <param name="input_taxa_file" type="data" format="txt" optional="true" label="input_taxa_file"
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33 help="summarized taxa file with samplecounts by taxonomy (resulting file from summarize_taxa.py)"/>
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34 <param name="ball_scale" type="float" value="1.0" label="ball_scale"
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35 help="scale factor for the size of each ball in the plots [default: 1.0]"/>
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36 <param name="arrow_line_color" type="text" value="white" label="arrow_line_color"
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37 help="arrow line color forprocrustes analysis. [default: white]"/>
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38 <param name="arrow_head_color" type="text" value="red" label="arrow_head_color"
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39 help="arrow head color forprocrustes analysis. [default: red]"/>
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40 </inputs>
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41 <outputs>
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42 <data format="txt" name="output_fp"/>
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43 </outputs>
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44 <tests>
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45 </tests>
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46 <help>For more information, see make_prefs_file_ in the Qiime documentation.
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47
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48 Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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49
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50 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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51
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52 .. _make_prefs_file: http://qiime.org/scripts/make_prefs_file.html</help>
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53 </tool>
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54
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