Mercurial > repos > ebi-gxa > garnett_check_markers
annotate garnett_check_markers.xml @ 0:d2aace2bb87f draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
author | ebi-gxa |
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date | Wed, 08 Apr 2020 06:17:49 -0400 |
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children | c00e672eadbc |
rev | line source |
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0
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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1 <tool id="garnett_check_markers" name="Garnett - check markers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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2 <description>Check marker file to filter out markers of suboptimal quality</description> |
d2aace2bb87f
"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> |
d2aace2bb87f
"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> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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5 </macros> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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6 <expand macro="requirements" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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7 <command detect_errors="exit_code"><![CDATA[ |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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8 garnett_check_markers.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --cds-gene-id-type '${cds_gene_id_type}' --marker-file-gene-id-type '${marker_file_gene_id_type}' --marker-output-path '${marker_output_path}' --plot-output-path '${plot_output_path}' --propogate-markers '${propogate_markers}' --classifier-gene-id-type '${classifier_gene_id_type}' |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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9 ]]></command> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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10 <inputs> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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11 <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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12 <param type="data" name="marker_file_path" format="txt" label="Marker file path" help="File with marker genes specifying cell types. |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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13 See https://cole-trapnell-lab.github.io/garnett/docs/#constructing-a-marker-file for specification of the file format" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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14 <param type="text" name="database" label="gene database" value="org.Hs.eg.db" help="argument for Bioconductor AnnotationDb-class package used for converting gene IDs" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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15 <param type="text" name="cds_gene_id_type" label="CDS gene id type" value="ENSEMBL" help="Format of the gene IDs in your CDS object" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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16 <param type="text" name="marker_file_gene_id_type" label="Marker gene id type" value="ENSEMBL" help="Format of the gene IDs in your marker file" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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17 <param type="boolean" name="propogate_markers" checked="true" label="propogate markers" help="Should markers from child nodes of a cell type be used |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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18 in finding representatives of the parent type?" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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19 <param type="text" name="classifier_gene_id_type" label="Classifier gene ID type" value="ENSEMBL" help="The type of gene ID that will be used in the classifier. If possible for your organism, this should be 'ENSEMBL', which is the default." /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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20 </inputs> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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21 <outputs> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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22 <data name="marker_output_path" format="txt" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
parents:
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23 <data name="plot_output_path" format="png" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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24 </outputs> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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25 <tests> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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26 <test> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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27 <param name="cds_object" value="garnett_cds.rds" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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28 <param name="marker_file_path" value="markers_transformed.txt" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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29 <output name="marker_output_path" value="marker_check.txt" compare="sim_size" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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30 </test> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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31 </tests> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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32 <help><![CDATA[ |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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33 @HELP@ |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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34 |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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35 @VERSION_HISTORY@ |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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36 ]]></help> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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37 <expand macro="citations" /> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
ebi-gxa
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38 </tool> |
d2aace2bb87f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
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39 |