Mercurial > repos > iuc > qiime_make_otu_heatmap

comparison make_otu_heatmap.xml @ 5:06cb29d26718 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:32:00 -0400
parents a3d1104d090c
children dd5418b9a32c
comparison
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4:11a2b9162be2 5:06cb29d26718
1 <tool id="qiime_make_otu_heatmap" name="Plot heatmap of OTU table" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_make_otu_heatmap" name="Plot heatmap of OTU table" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description>(make_otu_heatmap)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>make_otu_heatmap.py --version</version_command> 7 <version_command>make_otu_heatmap.py --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 make_otu_heatmap.py 9 make_otu_heatmap.py
10 --otu_table_fp '$otu_table_fp' 10 --otu_table_fp '$otu_table_fp'
11 11
12 #if $imagetype == "pdf" 12 #if $imagetype == "pdf"
13 --output_fp '$pdf_output_fp' 13 --output_fp '$pdf_output_fp'
14 #else if $imagetype == "png" 14 #else if $imagetype == "png"
15 --output_fp '$png_output_fp' 15 --output_fp '$png_output_fp'
16 #else if $imagetype == "svg" 16 #else if $imagetype == "svg"
17 --output_fp '$svg_output_fp' 17 --output_fp '$svg_output_fp'
18 #end if 18 #end if
19 19
20 #if $otu_tree 20 #if $otu_tree
21 --otu_tree '$otu_tree' 21 --otu_tree '$otu_tree'
22 #end if 22 #end if
23 #if $map_fname 23 #if $map_fname
24 --map_fname '$map_fname' 24 --map_fname '$map_fname'
25 #end if 25 #end if
26 #if str($category) != '' 26 #if str($category) != ''
27 --category '$category' 27 --category '$category'
28 #end if 28 #end if
29 #if $sample_tree 29 #if $sample_tree
30 --sample_tree '$sample_tree' 30 --sample_tree '$sample_tree'
31 #end if 31 #end if
32 --imagetype '$imagetype' 32 --imagetype '$imagetype'
33 $no_log_transform 33 $no_log_transform
34 $suppress_row_clustering 34 $suppress_row_clustering
35 $suppress_column_clustering 35 $suppress_column_clustering
36 $absolute_abundance 36 $absolute_abundance
37 37
38 #if str($ad.select) == "yes": 38 #if str($ad.select) == "yes":
39 --color_scheme '$ad.color_scheme' 39 --color_scheme '$ad.color_scheme'
40 --width '$ad.width' 40 --width '$ad.width'
41 --height '$ad.height' 41 --height '$ad.height'
42 --dpi '$ad.dpi' 42 --dpi '$ad.dpi'
43 --obs_md_category '$ad.obs_md_category' 43 --obs_md_category '$ad.obs_md_category'
44 #if str($ad.obs_md_level) != '' 44 #if str($ad.obs_md_level) != ''
45 --obs_md_level '$ad.obs_md_level' 45 --obs_md_level '$ad.obs_md_level'
46 #end if 46 #end if
47 #end if 47 #end if
48 ]]></command> 48 ]]></command>
49 <inputs> 49 <inputs>
50 <param argument="--otu_table_fp" type="data" format="biom1" label="Input OTU table"/> 50 <param argument="--otu_table_fp" type="data" format="biom1" label="Input OTU table"/>
51 <param argument="--otu_tree" type="data" format="txt" label="Tree file to be used for sorting OTUs in the heatmap" name="otu_tree" optional="True"/> 51 <param argument="--otu_tree" type="data" format="txt" optional="true" label="Tree file to be used for sorting OTUs in the heatmap"/>
52 <param argument="--map_fname" type="data" format="txt" label="Metadata mapping file to be used for sorting" optional="True"/> 52 <param argument="--map_fname" type="data" format="txt" optional="true" label="Metadata mapping file to be used for sorting"/>
53 <param argument="--category" type="text" label="Metadata category for sorting samples" help=" Samples will be clustered within each category level using euclidean UPGMA" optional="True"/> 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"/>
54 <param argument="--sample_tree" type="data" format="txt" 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." optional="True"/> 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."/>
55 <param argument="--imagetype" type="select" label="Type of image to produce"> 55 <param argument="--imagetype" type="select" label="Type of image to produce">
56 <option value="pdf" selected="True">PDF</option> 56 <option value="pdf" selected="true">PDF</option>
57 <option value="png">PNG</option> 57 <option value="png">PNG</option>
58 <option value="svg">SVG</option> 58 <option value="svg">SVG</option>
59 </param> 59 </param>
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."/> 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."/>
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."/> 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."/>
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."/> 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."/>
63 <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="False" label="Do not normalize samples to sum to 1?"/> 63 <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="Do not normalize samples to sum to 1?"/>
64 <conditional name="ad"> 64 <conditional name="ad">
65 <param name="select" type="select" label="Show advanced options"> 65 <param name="select" type="select" label="Show advanced options">
66 <option value="no" selected="True">No</option> 66 <option value="no" selected="true">No</option>
67 <option value="yes">Yes</option> 67 <option value="yes">Yes</option>
68 </param> 68 </param>
69 <when value="no"/> 69 <when value="no"/>
70 <when value="yes"> 70 <when value="yes">
71 <param argument="--color_scheme" type="select" label="Color scheme for figure" help="More details in http://matplotlib.org/examples/color/colormaps_reference.html"> 71 <param argument="--color_scheme" type="select" label="Color scheme for figure" help="More details in http://matplotlib.org/examples/color/colormaps_reference.html">