Mercurial > repos > ebi-gxa > scpred_get_std_output

annotate scpred_get_std_output.xml @ 3:43ce84bd1d9a draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 2f718294665c9d01702ad765904972f463154cd6"
author ebi-gxa
date Fri, 01 May 2020 10:14:28 -0400
parents 138d00a58412
children d276a8dd73c7
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43ce84bd1d9a "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 2f718294665c9d01702ad765904972f463154cd6"
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1 <tool id="scpred_get_std_output" name="Scpred - get output in standard format" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>This method allows to export predicted labels in a standardised format, simplifying downstream analyses.</description>
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3 <macros>
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4 <import>scpred_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 scpred_get_std_output.R --predictions-file "${predictions_file}" --get-scores "${get_scores}" --classifier '${classifier}' --output-table "${output_table}"
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9 ]]></command>
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10 <inputs>
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11 <param type="data" name="predictions_file" label="Predictions file" format="txt" help="Path to the predictions file in text format" />
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12 <param type="data" name="classifier" label="Classifier object" format="rdata" help="Path to the classifier object used to obtain predictions" />
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13 <param type="boolean" checked="false" name="get_scores" label="Get scores" help="Boolean: should the prediction scores be included? default: FALSE" />
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14 </inputs>
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15 <outputs>
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16 <data name="output_table" format="txt" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="predictions_file" value="predictions_table.txt" />
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21 <param name="get_scores" value="TRUE" />
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22 <output name="output_table" file="scpred_output_tbl.txt" compare="sim_size"/>
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23 </test>
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24 </tests>
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25 <help><![CDATA[
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26 @HELP@
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28 @VERSION_HISTORY@
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29 ]]></help>
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30 <expand macro="citations" />
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31 </tool>