Mercurial > repos > iuc > calculate_contrast_threshold

annotate calculate_contrast_threshold.xml @ 0:7371bb087d86 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
author iuc
date Wed, 11 Sep 2019 09:28:55 -0400
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7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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1 <tool id="calculate_contrast_threshold" name="Calculate Contrast threshold" version="1.0.0">
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2 <description>from tag pileup CDT
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="1.15.4">numpy</requirement>
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6 <requirement type="package" version="3.7.4">python</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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10 python '$__tool_directory__/calculate_contrast_threshold.py' -i '$input_file'
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11
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12 ## Setting the quantile values properly.
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13 #if str($quantile_type.quantile_type_selector) == "b_option":
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14 -q '${quantile_type.quantile}'
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15 -m '${quantile_type.min_contrast}'
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16 #else if str($quantile_type.quantile_type_selector) == "t_option":
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17 -t '${quantile_type.quantile2}'
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18 #end if
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20 -d '$header' -s '$start_col' -r '$row_num' -l '$col_num'
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21 ]]>
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22 </command>
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24 <inputs>
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25 <param name="input_file" argument="-i" type="data" format="txt" label="Pileup Data Matrix "/>
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26 <param name="header" argument="-d" type="boolean" truevalue="T" falsevalue="F" checked="true" label="Does the input file have a Header ?" help="Standard CDT file have headers."/>
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27 <param name="start_col" argument="-s" type="integer" value="2" label="Valid Data Start Column" help="Valid data values start from this column"/>
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28 <param name="col_num" argument="-l" type="integer" value="300" label="Plot Width in pixels" help="Equal to the heatmap width you plan to create"/>
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29 <param name="row_num" argument="-r" type="integer" value="600" label="Plot Height in pixels" help="Equal to the heatmap height you plan to create"/>
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32 <conditional name="quantile_type">
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33 <param name="quantile_type_selector" type="select" display="radio" label="Choose the Contrast paramter">
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34 <option value="b_option" selected="true">Calculate thresholds from data (-b)</option>
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35 <option value="t_option">Enforce absolute thresholds (-t)
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36 </option>
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37 </param>
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39 <when value="b_option">
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40 <param name="quantile" argument="-b" type="float" min="0" max="100" value="95" label="Quantile" help="Enter your quantile value above."/>
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41 <param name="min_contrast" type="float" min="0" value="0" label="Minimum upper limit after Quantile calculation" help="This value will be used as the upper limit if the calculated quantile is below this value" argument="-m"/>
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42 </when>
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44 <when value="t_option">
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45 <param name="quantile2" argument="-t" type="float" min="0" value="0.0" label="Absolute tag threshold" help="Enter your custom tag threshold value above. takes real values (>= 0)"/>
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46 </when>
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47 </conditional>
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49 </inputs>
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51 <outputs>
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52 <data name="threshold_output" format="txt" from_work_dir="calcThreshold.txt"/>
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53 </outputs>
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54
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55 <tests>
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56 <test>
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57 <param name="input_file" value="sample.tabular"/>
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58 <param name="header" value="T"/>
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59 <param name="start_col" value="2"/>
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60 <param name="col_num" value="300"/>
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61 <param name="row_num" value="600"/>
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62 <conditional name="quantile_type">
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63 <param name="quantile_type_selector" value="b_option"/>
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64 <param name="quantile" value="95"/>
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65 <param name="min_contrast" value="5"/>
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66 </conditional>
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67 <output name="threshold_output" file="calcThreshold_b.txt" />
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68 </test>
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69 <test>
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70 <param name="input_file" value="sample.tabular"/>
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71 <param name="header" value="T"/>
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72 <param name="start_col" value="2"/>
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73 <param name="col_num" value="300"/>
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74 <param name="row_num" value="600"/>
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75 <conditional name="quantile_type">
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76 <param name="quantile_type_selector" value="t_option"/>
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77 <param name="quantile2" value="10.0"/>
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78 </conditional>
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79 <output name="threshold_output" file="calcThreshold_t.txt" />
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80 </test>
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81 </tests>
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82
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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83 <help>
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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84 <![CDATA[
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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85
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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86 **What it does**
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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87
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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88 ----
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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89
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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90 Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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91
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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92 **Choosing Plot Width & Height**
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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93
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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94 If your trying to create heatmaps with dimensions (Width x Height)px = (300 x 600)px. Use Plot width = 300, height = 600. This not only helps in generating unbiased heatmaps but also helps in reusing the calculated contrasts for heatmaps of same dimensions.
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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95
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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96 **Understanding contrast parameters**
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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97
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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98 `-b`
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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99
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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100 Calculates a percentile value (for example 95th percentile) from the input CDT data matrix to report upper-limit and lower-limit for setting heatmap contrasts.
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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101
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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102 Also can set a minimum upper-limit to fall-back, incase the calculated percentile is <= specified minimum.
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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103
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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104 `-t`
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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105
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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106 Takes the absolute value entered and reports an upper_limit and lower_limit.
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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107
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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108 ]]>
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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109 </help>
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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110
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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111 <citations>
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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112 <citation type="bibtex">
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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113 @unpublished{None,
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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114 author = {Kuntala, Prashant Kumar and Lai, William KM },
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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115 title = {None},
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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116 year = {None},
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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117 eprint = {None},
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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118 url = {http://www.pughlab.psu.edu/}
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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119 }</citation>
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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120 </citations>
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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121
7371bb087d86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold commit 6ba8e678f8cedabaf9b4759cddb81b8b3cd9ec31"
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122 </tool>