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annotate summarize_taxa_through_plots.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy" version="1.9.1">
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2 <description>summaries and plots</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements" />
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10 <version_command><![CDATA[
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11 summarize_taxa_through_plots.py --version
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12 ]]>
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13 </version_command>
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15 <command>
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16 <![CDATA[
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17 summarize_taxa_through_plots.py
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18 -i $otu_table_fp
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19 -o summarize_taxa_through_plots
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20
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21 #if $mapping_fp
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22 -m $mapping_fp
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23 #end if
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25 #if $mapping_category
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26 -c $mapping_category
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27 #end if
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29 $sort
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31 &&
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32
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33 mkdir -p $area_charts_html_report.files_path
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34 &&
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35 cp -r summarize_taxa_through_plots/taxa_summary_plots/area_charts.html $area_charts_html_report.files_path
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36 &&
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37 cp -r summarize_taxa_through_plots/taxa_summary_plots/charts $area_charts_html_report.files_path
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38 &&
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39 cp -r summarize_taxa_through_plots/taxa_summary_plots/css $area_charts_html_report.files_path
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40 &&
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41 cp -r summarize_taxa_through_plots/taxa_summary_plots/js $area_charts_html_report.files_path
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42 &&
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43 mv $area_charts_html_report.files_path/area_charts.html $area_charts_html_report
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44
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45 &&
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46 mkdir -p $bar_charts_html_report.files_path
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47 &&
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48 cp -r summarize_taxa_through_plots/taxa_summary_plots/bar_charts.html $bar_charts_html_report.files_path
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49 &&
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50 cp -r summarize_taxa_through_plots/taxa_summary_plots/charts $bar_charts_html_report.files_path
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51 &&
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52 cp -r summarize_taxa_through_plots/taxa_summary_plots/css $bar_charts_html_report.files_path
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53 &&
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54 cp -r summarize_taxa_through_plots/taxa_summary_plots/js $bar_charts_html_report.files_path
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55 &&
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56 mv $bar_charts_html_report.files_path/bar_charts.html $bar_charts_html_report
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57
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58 ]]>
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59 </command>
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60
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61 <inputs>
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62 <param name="otu_table_fp" type="data" format="biom,tabular,txt,tsv"
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63 label="Input OTU table" help="(-i/--otu_table_fp)"/>
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64
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65 <param name="mapping_fp" type="data" format="tabular,tsv,csv"
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66 label="Input metadata mapping (optional)" help="(-m, --mapping_fp)"
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67 optional="True"/>
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68
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69 <param name="mapping_category" type="text" value="" label="Category to
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70 use to summarize OTU table" help="(-c/--mapping_category)"
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71 optional="True"/>
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72
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73 <param name="sort" type="boolean" label="Sort OTU table?"
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74 truevalue="--sort" falsevalue="" selected="False"
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75 help="(-s/--sort)" />
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76 </inputs>
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77
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78 <outputs>
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79 <data name="L2_tab" format="tabular"
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80 from_work_dir="summarize_taxa_through_plots/*_L2.txt"
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81 label="${tool.name} on ${on_string}: L2 tab">
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82 <filter>"2" in level and suppress_classic_table_output is False</filter>
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83 </data>
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84
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85 <data name="L3_tab" format="tabular"
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86 from_work_dir="summarize_taxa_through_plots/*_L3.txt"
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87 label="${tool.name} on ${on_string}: L3 tab">
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88 <filter>"3" in level and suppress_classic_table_output is False</filter>
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89 </data>
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90
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91 <data name="L4_tab" format="tabular"
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92 from_work_dir="summarize_taxa_through_plots/*_L4.txt"
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93 label="${tool.name} on ${on_string}: L4 tab">
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94 <filter>"4" in level and suppress_classic_table_output is False</filter>
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95 </data>
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96
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97 <data name="L5_tab" format="tabular"
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98 from_work_dir="summarize_taxa_through_plots/*_L5.txt"
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99 label="${tool.name} on ${on_string}: L5 tab">
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100 <filter>"5" in level and suppress_classic_table_output is False</filter>
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101 </data>
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102
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103 <data name="L6_tab" format="tabular"
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104 from_work_dir="summarize_taxa_through_plots/*_L6.txt"
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105 label="${tool.name} on ${on_string}: L6 tab">
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106 <filter>"6" in level and suppress_classic_table_output is False</filter>
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107 </data>
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108
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109 <data name="bar_charts_html_report" format="html"
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110 label="${tool.name} on ${on_string}: Bar charts">
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111 <filter>'bar' is chart_type</filter>
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112 </data>
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113
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114 <data name="area_charts_html_report" format="html"
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115 label="${tool.name} on ${on_string}: Area charts">
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116 <filter>'area' is chart_type</filter>
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117 </data>
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118 </outputs>
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119
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120 <tests>
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121 <test>
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122 </test>
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123 </tests>
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124
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125 <help><![CDATA[
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126 **What it does**
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127
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128 This tool summarizes OTU by Category (optional), summarizes taxonomy and plots
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129 taxonomy summary.
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130
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131 More information about this tool is available on
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132 `QIIME documentation <http://qiime.org/scripts/summarize_taxa_through_plots.html>`_.
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133 ]]>
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134 </help>
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135
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136 <citations>
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137 <expand macro="citations" />
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138 </citations>
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139
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140 </tool>