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annotate ct_get_empirical_dist.xml @ 4:44a6618cce59 draft

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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 15:05:11 +0000
parents 6fc67b8caa21
children a749b4edecd6
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1 <tool id="ct_get_empirical_dist" name="Cell types - get empirical distribution" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>Get empirical distribution for tool performance table</description>
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3 <macros>
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4 <import>ct_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[
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8
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9 ln -s $'${ontology_graph}' cl-basic.obo;
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11 get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores \${GALAXY_SLOTS:-1} --ontology-graph cl-basic.obo --output-path "${output_list_path}"
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12
2
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13 #if $parallel
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14 --parallel "${parallel}"
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15 #end if
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16 #if $exclusions
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17 --exclusions "${exclusions}"
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18 #end if
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19 #if $exclusions
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20 --semantic-sim-metric "${sem_sim_metric}"
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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_ref_file" label="Input reference file" format="txt" help="Text file with reference cell labels" />
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25 <param type="data" name="exclusions" format="yml" label="Exclusions file" help="YML file with excluded/unlabelled terms" />
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26 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
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27 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
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28 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
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29 <param type="integer" name="num_iter" value='5' label="Number of iterations" help="Number of simulations to generate empirical CDF" />
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30 <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" />
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31 <param type="text" name="sem_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
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32 </inputs>
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33 <outputs>
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34 <data name="output_list_path" format="rdata" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input_ref_file" value="reference_sdrf.tsv" />
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39 <param name="label_col_ref" value="Sample.Characteristic.cell.type." />
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40 <param name="ontology_graph" value="cl-basic.obo" />
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41 <param name="exclusions" value="exclusions.yml" />
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42 <param name="parallel" value="TRUE" />
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43 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
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44 <output name="output_list_path" file="empirical_dist_list.rds" compare="sim_size" />
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 @HELP@
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49
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50 @VERSION_HISTORY@
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51 ]]></help>
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52 <expand macro="citations" />
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53 </tool>