Mercurial > repos > galaxyp > quantp
comparison quantp.xml @ 2:ed0bb50d7ffe draft
planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
| author | galaxyp |
|---|---|
| date | Wed, 09 Jan 2019 16:59:24 -0500 |
| parents | bcc7a4c4cc29 |
| children | a8bedebab467 |
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| 1:bcc7a4c4cc29 | 2:ed0bb50d7ffe |
|---|---|
| 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 |