Mercurial > repos > ebi-gxa > garnett_transform_markers

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85476ee7f3b1d96e9d0afb972af1aaa67d990ce4"
author ebi-gxa
date Mon, 27 Apr 2020 11:18:45 -0400
parents b35eef6b1fcc
children
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3
1dc49d16e96c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85476ee7f3b1d96e9d0afb972af1aaa67d990ce4"
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1 <tool id="garnett_transform_markers" name="Garnett - transform markes" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>Transform marker files from Single Cell Expression Atlas format to that compatible with Garnett</description>
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3 <macros>
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4 <import>garnett_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
1
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8 transform_marker_file.R --input-marker-file '${input_marker_file}' --marker-list '${marker_list}' --garnett-marker-file '${garnett_marker_file}'
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9
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10 #if $pval_col
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11 --pval-col '${pval_col}'
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12 #end if
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13 #if $pval_threshold
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14 --pval-threshold '${pval_threshold}'
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15 #end if
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16 #if $groups_col
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17 --groups-col '${groups_col}'
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18 #end if
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19 #if $gene_names
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20 --gene-names '${gene_names}'
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21 #end if
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22 ]]></command>
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23 <inputs>
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24 <param type="data" name="input_marker_file" format="txt" label="Input marker file" help="Path to the SCXA-style marker gene file in .txt format" />
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25 <param type="text" name="pval_col" value="pvals" label="p-value column name" help="Column name of marker p-values" />
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26 <param type="float" name="pval_threshold" value="0.05" label="p-value threshold" help="Cut-off p-value for marker genes" />
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27 <param type="text" name="groups_col" value="groups" label="groups column" help="Column name of cell groups (i.e. cluster IDs or cell types) in marker file" />
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28 <param type="text" name="gene_names" value="names" label="gene names" help="Column containing gene names in marker file" />
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29 </inputs>
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30 <outputs>
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31 <data name="garnett_marker_file" format="txt" />
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32 <data name="marker_list" format="rdata" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input_marker_file" value="ref_marker_genes.txt" />
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37 <param name="marker_list" value="marker_list.rds" />
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38 <output name="garnett_marker_file" file="markers_transformed.txt" compare="sim_size"/>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 @HELP@
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44 @VERSION_HISTORY@
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45 ]]></help>
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46 <expand macro="citations" />
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47 </tool>
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