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comparison quantp.xml @ 2:1b11db35d7b5 draft

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planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
author galaxyp
date Wed, 09 Jan 2019 16:58:43 -0500
parents dec87511835e
children 9c70b9a95406
comparison
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1:dec87511835e 2:1b11db35d7b5
1 <tool id="quantp" name="QuanTP" version="1.1.0"> 1 <tool id="quantp" name="QuanTP" version="1.1.1">
2 <description>Correlation between protein and transcript abundances</description> 2 <description>Correlation between protein and transcript abundances</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.10.4">r-data.table</requirement> 4 <requirement type="package" version="1.10.4">r-data.table</requirement>
5 <requirement type="package" version="3.0.1">r-gplots</requirement> 5 <requirement type="package" version="3.0.1">r-gplots</requirement>
6 <requirement type="package" version="0.7.6">r-dplyr</requirement> 6 <requirement type="package" version="0.7.6">r-dplyr</requirement>
7 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 7 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
8 <requirement type="package" version="0.4.5">r-ggfortify</requirement> 8 <requirement type="package" version="0.4.5">r-ggfortify</requirement>
9 <requirement type="package" version="4.8.0">r-plotly</requirement> 9 <requirement type="package" version="4.8.0">r-plotly</requirement>
10 <requirement type="package" version="0.6.1.2">r-d3heatmap</requirement> 10 <requirement type="package" version="0.6.1.1">r-d3heatmap</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 Rscript '$__tool_directory__/quantp.r' 13 Rscript '$__tool_directory__/quantp.r'
14 $experiment_design_option.sample_type 14 $experiment_design_option.sample_type
15 $experiment_design_option.method_type 15 $experiment_design_option.method_type
112 <has_text text="SAMPLE DISTRIBUTION" /> 112 <has_text text="SAMPLE DISTRIBUTION" />
113 <has_text text="plotly" /> 113 <has_text text="plotly" />
114 </assert_contents> 114 </assert_contents>
115 </output> 115 </output>
116 </test> 116 </test>
117 <test>
118 <conditional name="experiment_design_option">
119 <param name="sample_type" value="logfold"/>
120 <param name="correction_method" value="BH"/>
121 <param name="volcano_with" value="pval"/>
122 </conditional>
123 <param name="pe_exp" value="mouse_protein_log_data.txt" ftype="tabular" />
124 <param name="te_exp" value="mouse_transcript_log_data.txt" ftype="tabular" />
125 <param name="cooksd_upper" value="4"/>
126 <param name="nclust" value="4"/>
127 <param name="hm_nclust" value="5"/>
128 <output name="html_file">
129 <assert_contents>
130 <has_text text="SAMPLE DISTRIBUTION" />
131 <has_text text="plotly" />
132 </assert_contents>
133 </output>
134 </test>
117 </tests> 135 </tests>
118 <help><![CDATA[ 136 <help><![CDATA[
119 137
120 **What it does** 138 **What it does**
121 139