Mercurial > repos > ebi-gxa > update_marker_file

annotate update_marker_file.xml @ 0:8ee96cde3643 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
author ebi-gxa
date Wed, 08 Apr 2020 06:32:25 -0400
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children 5036928f60bc
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8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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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"
ebi-gxa
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3 <macros>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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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"
ebi-gxa
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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"
ebi-gxa
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7 <command detect_errors="exit_code"><![CDATA[
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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8 update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}' --summary-col '${summary_col}' --cell-type-col '${cell_type_col}' --gene-id-col '${gene_id_col}' --updated-marker-file '${updated_marker_file}'
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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9 ]]></command>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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10 <inputs>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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11 <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"
ebi-gxa
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12 <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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13 <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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14 <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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15 <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"
ebi-gxa
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16 </inputs>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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17 <outputs>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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18 <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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19 </outputs>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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20 <tests>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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21 <test>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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22 <param name="marker_list_obj" value="marker_list.rds" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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23 <param name="marker_check_file" value="marker_check.txt" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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24 <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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25 </test>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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26 </tests>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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27 <help><![CDATA[
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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28 @HELP@
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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29
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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30 @VERSION_HISTORY@
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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31 ]]></help>
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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32 <expand macro="citations" />
8ee96cde3643 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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33 </tool>