Mercurial > repos > ebi-gxa > ct_combine_tool_outputs
annotate ct_combine_tool_outputs.xml @ 5:f2e01e023137 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dda3554de219b904e9bef7bbc0ca78fc9622a691"
author | ebi-gxa |
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date | Thu, 23 Jul 2020 11:59:15 -0400 |
parents | 44b6219cba2d |
children | 844689a7f66e |
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5
f2e01e023137
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dda3554de219b904e9bef7bbc0ca78fc9622a691"
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1 <tool id="ct_combine_tool_outputs" name="Cell types - combine tools outputs" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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2 <description>Combine predictions for single tool from multiple datasets</description> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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3 <macros> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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4 <import>ct_macros.xml</import> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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5 </macros> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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6 <expand macro="requirements" /> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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7 <command detect_errors="exit_code"><![CDATA[ |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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8 mkdir -p input_dir; |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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9 #for $table in $input_tables: |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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10 cp '$table' input_dir/; |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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11 #end for |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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12 |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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13 combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --scores "${scores}" --output-table "${output_table}" |
a565cf41330b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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14 |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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15 #if $exclusions |
a565cf41330b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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16 --exclusions "${exclusions}" |
a565cf41330b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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17 #end if |
a565cf41330b
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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18 ]]></command> |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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19 <inputs> |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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20 <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="txt" help="Standardised tables obtained from multiple classifiers" /> |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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21 <param type="integer" name="top_labels_num" label="Number of top labels" value='3' help="Number of top labels to select" /> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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22 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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23 <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" /> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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24 </inputs> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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25 <outputs> |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
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26 <data name="output_table" format="txt" /> |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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27 </outputs> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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28 <tests> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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29 <test> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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30 <param name="input_tables" value="prod_outputs_scpred/E-MTAB-6386_scpred_final-labs.tsv,prod_outputs_scpred/OTHER-DATASET_scpred_final-labs.tsv" /> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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31 <param name="scores" value="TRUE" /> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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32 <param name="exclusions" value="exclusions.yml" /> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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33 <output name="output_table" file="combined_results.tsv" compare="sim_size" /> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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34 </test> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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35 </tests> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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36 <help><![CDATA[ |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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37 @HELP@ |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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38 |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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39 @VERSION_HISTORY@ |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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40 ]]></help> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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41 <expand macro="citations" /> |
7c7d1ef36bf6
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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42 </tool> |