Mercurial > repos > ppericard > mixomics_blocksplsda

annotate circleCor.xml @ 3:0a3c83f2197a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author ppericard
date Fri, 25 Oct 2019 07:10:59 -0400
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1 <tool id="circleCor" name="circleCor" version="0.2.0" profile="16.04" workflow_compatible="true">
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3 <description></description>
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5 <requirements>
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6 <requirement type="package">r-base</requirement>
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7 <requirement type="package" version="0.4">r-ellipse</requirement>
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8 <requirement type="package" version="2.0">r-argparse</requirement>
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9 <requirement type="package" version="1.1">r-rcolorbrewer</requirement>
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11 <!-- <requirement type="package" version="6.8">bioconductor-mixomics</requirement> -->
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12 </requirements>
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14 <stdio>
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15 <!-- <exit_code range="1:" level="fatal" /> -->
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16 </stdio>
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18 <command detect_errors="aggressive">
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19 <![CDATA[
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20 Rscript
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21 ${__tool_directory__}/circleCor_wrapper.R
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22 --input_rdata ${input_rdata}
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23 --blocks_vec ${select_blocks.value}
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24 --responses_var ${select_responses_var}
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25 --x_min ${x_min}
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26 --x_max ${x_max}
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27 --y_min ${y_min}
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28 --y_max ${y_max}
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29 --output_var ${output_var}
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30 --output_pdf ${output_pdf}
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31 ]]>
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32 </command>
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34 <inputs>
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35 <param name="input_rdata" type="data" format="rdata" label="Input RData file from block.SPLSDA"/>
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36 <param name="blocks_vec_list" type="data" format="tabular" label="List of blocks vector"/>
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37 <param name="select_blocks" type="select" label="Blocks">
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38 <options from_dataset="blocks_vec_list">
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39 <column name="value" index="0"/>
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40 <filter type="unique_value" column="0"/>
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41 <filter type="sort_by" name="sorted_value" column="0"/>
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42 </options>
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43 </param>
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44 <param name="responses_var_list" type="data" format="tabular" label="List of response variables"/>
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45 <param name="select_responses_var" type="select" display="checkboxes" multiple="true" label="Response variables">
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46 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
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47 <options from_dataset="responses_var_list">
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48 <column name="value" index="0"/>
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49 <filter type="unique_value" column="0"/>
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50 <filter type="sort_by" name="sorted_value" column="0"/>
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51 </options>
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52 </param>
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53 <param name="x_min" type="float" value="-1" min="-1" max="1" label="X min" help="" />
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54 <param name="x_max" type="float" value="1" min="-1" max="1" label="X max" help="" />
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55 <param name="y_min" type="float" value="-1" min="-1" max="1" label="Y min" help="" />
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56 <param name="y_max" type="float" value="1" min="-1" max="1" label="Y max" help="" />
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57 </inputs>
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59 <outputs>
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60 <data name="output_var" format="tabular" label="${tool.name}_var.tsv" />
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61 <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
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62 </outputs>
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64 <tests>
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65 </tests>
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67 <help>
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68 </help>
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70 </tool>