Mercurial > repos > ebi-gxa > scmap_get_std_output
annotate scmap_get_std_output.xml @ 7:2f63b1cd9122 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author | ebi-gxa |
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date | Fri, 27 Nov 2020 13:42:47 +0000 |
parents | 0d713384d8d8 |
children | 601a933714f1 |
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0d713384d8d8
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 824146613fdab1de5bf430e01422417a720fe3f2"
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1 <tool id="scmap_get_std_output" name="Scmap get standard output" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
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5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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2 <description>Create 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> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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3 <macros> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
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4 <import>scmap_macros.xml</import> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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5 </macros> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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6 <expand macro="requirements" /> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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7 <command detect_errors="exit_code"><![CDATA[ |
7
2f63b1cd9122
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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8 scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}" --tool '${tool}' --sim-col-name "${sim_col_name}" |
2f63b1cd9122
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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9 #if $index |
2f63b1cd9122
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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10 --index "${index}" |
2f63b1cd9122
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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11 #end if |
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5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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12 ]]></command> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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13 <inputs> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
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14 <param type="data" name="input_predictions_file" label="Scmap predictions file in text format" format="txt" help="Path to the predictions file in text format" /> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
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15 <param type="boolean" name="include_scores" checked="false" label="Should prediction scores be included?" help="Boolean indicating whether similarity scores should be included in the final output" /> |
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2f63b1cd9122
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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16 <param type="data" name="index" label="Scmap index object" optional="true" format="rdata" help="Scmap index object in rdata format" /> |
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656c588b718c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
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17 <param type="select" name="tool" label="Tool used (cell/cluster)" help="What tool was used - scmap-cell or scmap-cluster?"> |
656c588b718c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
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18 <option value="scmap-cell">Scmap-cell</option> |
656c588b718c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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19 <option value="scmap-cluster">Scmap-cluster</option> |
656c588b718c
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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20 </param> |
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5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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21 <param type="text" name="sim_col_name" value="scmap_cluster_siml" label="Column name of similarity scores" help="Name of column that contains distances between clusters/cells" /> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
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22 </inputs> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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23 <outputs> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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24 <data name="output_predictions_file" format="txt" /> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
ebi-gxa
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25 </outputs> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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26 <tests> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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27 <test> |
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2f63b1cd9122
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
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28 <param name="input_predictions_file" value="closest_cells_clusters.tsv" /> |
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5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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29 <param name="include_scores" value="TRUE" /> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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30 <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" /> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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31 </test> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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32 </tests> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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33 <help><![CDATA[ |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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34 Generate output tables in tab-separated format compatible with input specified in cell-types-analysis package: https://github.com/ebi-gene-expression-group/cell-types-analysis. |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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35 See the example snippet below: |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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36 ________________________________________ |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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37 | cell_id | predicted_label | score | |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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38 | ERR2632411 | memory B cell | 0.8 | |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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39 ... |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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40 |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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41 @VERSION_HISTORY@ |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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42 ]]></help> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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43 <expand macro="citations" /> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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44 </tool> |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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45 |
5f95950c3959
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 542b6e6848acedbbedb6fa2d4b44c8d476597cdd"
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46 |