Mercurial > repos > ebi-gxa > scpred_get_std_output

annotate scpred_get_std_output.xml @ 1:8bd9131f429d draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 3fc448754d6720855f781caa7938e33d3961b092"
author ebi-gxa
date Thu, 16 Apr 2020 09:29:17 +0000
parents 92a7580a73f6
children f35b359eece0
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92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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1 <tool id="scpred_get_std_output" name="Get output in standard format" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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2 <description>This method allows to export predicted labels in a standardised format, simplifying downstream analyses.</description>
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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3 <macros>
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4 <import>scpred_macros.xml</import>
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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5 </macros>
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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6 <expand macro="requirements" />
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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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}" --output-table "${output_table}"
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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9 ]]></command>
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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10 <inputs>
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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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" />
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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12 <param type="boolean" checked="false" name="get_scores" label="Get scores" help="Boolean: should the prediction scores be included? default: FALSE" />
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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13 </inputs>
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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14 <outputs>
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15 <data name="output_table" format="txt" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="predictions_file" value="predictions_table.txt" />
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20 <param name="get_scores" value="TRUE" />
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21 <output name="output_table" file="scpred_output_tbl.txt" compare="sim_size"/>
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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22 </test>
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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23 </tests>
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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24 <help><![CDATA[
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25 @HELP@
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26
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27 @VERSION_HISTORY@
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28 ]]></help>
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29 <expand macro="citations" />
92a7580a73f6 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 6ea13bbd7294b94201a5d776307b3f0742847db1"
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30 </tool>