Mercurial > repos > ebi-gxa > monocle3_topmarkers

annotate monocle3-topmarkers.xml @ 0:bc2df96ef963 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
author ebi-gxa
date Thu, 14 May 2020 17:17:27 -0400
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bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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1 <?xml version="1.0" encoding="utf-8"?>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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2 <tool id="monocle3_topmarkers" name="Monocle3 top markers" version="0.1.5+galaxy0" profile="@PROFILE@">
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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3 <description>for cell groups</description>
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4 <macros>
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5 <import>monocle3-macros.xml</import>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="0.0.8">monocle3-cli</requirement>
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '$input_object' input.rds;
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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12 #if $ref_cells.source == 'file' and $ref_cells.file
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13 list_of_cells=\$(cat $ref_cells.file | tr '\n' ',')
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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14 #end if
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15 LANG=en_US.UTF-8 monocle3 topMarkers
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16 --input-object-format cds3
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17 #if $filter_fraction_expression
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18 --filter-fraction-expression '$filter_fraction_expression'
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19 #end if
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20 #if $top_n_markers
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21 --top-n-markers '$top_n_markers'
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22 #end if
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23 #if $plot_top_markers
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24 --plot-top-markers top_markers.pdf
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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25 #end if
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26 #if $save_full_markers
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27 --save-full-markers full_markers.tsv
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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28 #end if
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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29 #if $ref_cells.source == 'file' and $ref_cells.file
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30 --reference-cells \$list_of_cells
bc2df96ef963 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c388aa3bb719eff471508b6f01cae8583ee7bb1d"
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31 #end if
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32 #if $ref_cells.source == 'number' and $ref_cells.number
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33 --reference-cells '$ref_cells.number'
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34 #end if
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35 #if $marker_sig_test
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36 --marker-sig-test
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37 #end if
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38 #if $genes_to_test_per_group
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39 --genes-to-test-per-group '$genes_to_test_per_group'
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40 #end if
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41 #if $group_cells_by
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42 --group-cells-by '$group_cells_by'
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43 #end if
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44 --cores \${GALAXY_SLOTS:-1}
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45 --introspective
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46
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47 input.rds
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48 output.tsv
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49 ]]></command>
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50 <inputs>
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51 <param label="Input Object" name="input_object" type="data" format='rdata' help="Input file with monocle3 object cds3 in RDS"/>
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52 <conditional name="ref_cells">
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53 <param label="Reference cells source" name="source" type="select" argument="--reference-cells" help="(Optional) Set of cells to be considered as reference for marker significance test. Accelerates the marker significance test at some cost in sensitivity.">
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54 <option value="file">File</option>
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55 <option value="number">Number of cells</option>
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56 </param>
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57 <when value="file">
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58 <param label="Reference cells file" name="file" optional="true" argument="--reference-cells" type="data" format='txt' help="File with cells to be used as reference cells."/>
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59 </when>
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60 <when value="number">
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61 <param label="Number of reference cells" name="number" optional="true" argument="--reference-cells" type="integer" help="Number of cells to be used as reference cells."/>
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62 </when>
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63 </conditional>
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64 <param label="Filter fraction for expression" optional='true' value="0.1" name="filter_fraction_expression" argument="--filter-fraction-expression" type="float" help="Filters the markers test result by this fraction of expression"/>
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65 <param label="Top-n-markers" optional='true' value="5" name="top_n_markers" argument="--top-n-markers" type="integer" help="The number of top marker genes to report in plots and in top markers list"/>
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66 <param label="Number of genes to test per group" optional='true' value="25" name="genes_to_test_per_group" argument="--genes-to-test-per-group" type="integer" help="how many genes of the top ranked specific genes by Jenson-Shannon, to do the more expensive regression test on"/>
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67 <param label="Group cell by" optional='true' value='cluster' name="group_cells_by" argument="--group-cells-by" type="text" help="Cell groups, choose from 'cluster', 'partition', or any categorical variable in `colData(cds)`"/>
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68 <param label="Use logistic regression to asses discriminatory power" value='false' name="marker_sig_test" argument="--marker-sig-test" type="boolean" checked='false' help="whether to assess the discriminative power of each marker through logistic regression. Can be slow, consider disabling to speed up top_markers()."/>
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69 <param label="Save full markers" value='false' name="save_full_markers" argument="--save-full-markers" type="boolean" checked='false' help="whether to generate the full markers list as well."/>
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70 <param label="Plot top markers" value='false' name="plot_top_markers" argument="--plot-top-markers" type="boolean" checked='true' help="whether to generate the top markers plot."/>
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71 </inputs>
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72
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73 <outputs>
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74 <data label="${tool.name} on ${on_string}: Top markers plot" name="top_markers_plot" format='pdf' from_work_dir='top_markers.pdf'>
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75 <filter>plot_top_markers</filter>
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76 </data>
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77 <data label="${tool.name} on ${on_string}: Full markers" name="full_markers" from_work_dir="full_markers.tsv" format='tabular'>
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78 <filter>save_full_markers</filter>
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79 </data>
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80 <data label="${tool.name} on ${on_string}: Top markers" name="top_markers_table" from_work_dir="output.tsv" format='tabular' />
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81 </outputs>
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82
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83 <tests>
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84 <test>
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85 <param name="input_object_file" value="input.rds"/>
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86 <param name="filter_fraction_expression" value="0.1"/>
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87 <output name="top_markers_table" file="top_markers_table.tsv" ftype="tsv" compare="sim_size"/>
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88 </test>
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89 </tests>
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90
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91 <help><![CDATA[
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92 ==========================================================
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93 Monocle3 top markers genes
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94 ==========================================================
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95
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96 Identify the genes most specifically expressed in groups of cells. See inline help for options.
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97
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98 @HELP@
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99
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100 @VERSION_HISTORY@
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101 ]]></help>
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102 <expand macro="citations"/>
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103 </tool>