Mercurial > repos > ebi-gxa > update_marker_file

annotate update_marker_file.xml @ 1:5036928f60bc draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
author ebi-gxa
date Fri, 24 Apr 2020 11:23:13 -0400
parents 8ee96cde3643
children
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8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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1 <tool id="update_marker_file" name="Garnett - update markers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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2 <description>Update marker file by filtering out suboptimal markers</description>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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3 <macros>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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4 <import>garnett_macros.xml</import>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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5 </macros>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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6 <expand macro="requirements" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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7 <command detect_errors="exit_code"><![CDATA[
1
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
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8 update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}' --updated-marker-file '${updated_marker_file}'
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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9
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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10 #if $summary_col
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
ebi-gxa
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11 --summary-col '${summary_col}'
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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12 #end if
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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13 #if $cell_type_col
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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14 --cell-type-col '${cell_type_col}'
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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15 #end if
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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16 #if $gene_id_col
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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17 --gene-id-col '${gene_id_col}'
5036928f60bc "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
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18 #end if
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19 ]]></command>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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20 <inputs>
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21 <param type="data" name="marker_list_obj" label="Marker list object" format="rdata" help="Serialised object containing markers list produced by garnett_transform_markers" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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22 <param type="data" name="marker_check_file" label="marker check file" format="txt" help="Path to the file with marker gene assessment done by garnett" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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23 <param type="text" name="summary_col" value="summary" label="Name of summary column" help="Marker gene assessment column name" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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24 <param type="text" name="cell_type_col" value="cell_type" label="Name of cell type column" help="Marker gene assessment column name" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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25 <param type="text" name="gene_id_col" value="gene_id" label="Name of gene id column" help="Gene id column name in marker assessment file" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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26 </inputs>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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27 <outputs>
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28 <data name="updated_marker_file" format="txt" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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29 </outputs>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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30 <tests>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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31 <test>
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32 <param name="marker_list_obj" value="marker_list.rds" />
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33 <param name="marker_check_file" value="marker_check.txt" />
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34 <output name="updated_marker_file" file="markers_upd.txt" compare="sim_size"/>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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35 </test>
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36 </tests>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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37 <help><![CDATA[
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38 @HELP@
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39
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40 @VERSION_HISTORY@
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41 ]]></help>
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42 <expand macro="citations" />
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43 </tool>