Mercurial > repos > ebi-gxa > garnett_get_std_output

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 660486ba0e1ef2f0195e7c6f75448221ba4640f7"
author ebi-gxa
date Tue, 28 Apr 2020 15:11:36 +0000
parents f5c6f85d35bf
children
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212976eeca07 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 660486ba0e1ef2f0195e7c6f75448221ba4640f7"
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1 <tool id="garnett_get_std_output" name="Garnett - get standard output" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>Get final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package</description>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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3 <macros>
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4 <import>garnett_macros.xml</import>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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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 garnett_get_std_output.R --input-object '${input_object}' --classifier '${classifier}' --output-file-path '${output_file_path}'
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9 ]]></command>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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10 <inputs>
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11 <param type="data" name="input_object" label="input CDS object" format="rdata" help="CDS object with predicted labels" />
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12 <param type="data" name="classifier" label="classifier object" format="rdata" help="Classifier object in rdata format" />
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c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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13 </inputs>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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14 <outputs>
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15 <data name="output_file_path" 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="input_object" value="cds_pred_labs.rds" />
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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20 <output name="output_file_path" value="garnett_output_tbl.txt" compare="sim_size" />
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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21 </test>
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22 </tests>
c5f5e64d9666 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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23 <help><![CDATA[
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24 @HELP@
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25
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26 @VERSION_HISTORY@
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27 ]]></help>
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28 <expand macro="citations" />
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29 </tool>