Mercurial > repos > ebi-gxa > scater_filter
comparison scater-filter.xml @ 0:32f886c22e75 draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 11:47:32 -0400 |
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-1:000000000000 | 0:32f886c22e75 |
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1 <tool id="scater_filter" name="Scater Filter" version="@TOOL_VERSION@+galaxy0"> | |
2 <description>cells and genes based on pre-calculated stats and QC metrics</description> | |
3 <macros> | |
4 <import>scater_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 scater-filter.R -i '${R_scater_qc}' -o '$R_scater_filtered' | |
9 #if $cell_parameters | |
10 #set cell_pars = ','.join([str($p['name']) for $p in $cell_parameters]) | |
11 -s '${cell_pars}' | |
12 #set cell_mins = ','.join([str($p['min']) for $p in $cell_parameters]) | |
13 -l '${cell_mins}' | |
14 #set cell_maxs = ','.join([str($p['max']) for $p in $cell_parameters]) | |
15 -j '${cell_maxs}' | |
16 #end if | |
17 #if $feature_parameters | |
18 #set ft_pars = ','.join([str($p['name']) for $p in $feature_parameters]) | |
19 -t '${ft_pars}' | |
20 #set ft_mins = ','.join([str($p['min']) for $p in $feature_parameters]) | |
21 -m '${ft_mins}' | |
22 #set ft_maxs = ','.join([str($p['max']) for $p in $feature_parameters]) | |
23 -n '${ft_maxs}' | |
24 #end if | |
25 #if $cells_use: | |
26 -c '$cells_use' | |
27 #end if | |
28 #if $cells_discard: | |
29 -C '$cells_discard' | |
30 #end if | |
31 #if $features_use: | |
32 -f '$features_use' | |
33 #end if | |
34 #if $output_selected_cells: | |
35 -u '$selected_cells' | |
36 #end if | |
37 #if $output_selected_features: | |
38 -v '$selected_featuers' | |
39 #end if | |
40 | |
41 ]]></command> | |
42 | |
43 <inputs> | |
44 <param name="R_scater_qc" type="data" format="rdata" | |
45 help="A serialized SingleCellExperiment object file in RDS format."/> | |
46 | |
47 <repeat name="cell_parameters" title="Parameters used to filter cells" min="0"> | |
48 <param name="name" type="text" value="total_features_by_counts" label="Name of the parameter to filter on" help="for example: total_features_by_counts, total_counts"> | |
49 <option value="total_features_by_counts">total_features_by_counts</option> | |
50 <option value="total_counts">total_counts</option> | |
51 </param> | |
52 <param name="min" type="float" value="-1e9" label="Min value"/> | |
53 <param name="max" type="float" value="1e9" label="Max value"/> | |
54 </repeat> | |
55 | |
56 <repeat name="feature_parameters" title="Parameters used to filter features" min="0"> | |
57 <param name="name" type="text" value="n_cells_by_counts" label="Name of the parameter to filter on" help="for example: n_cells_by_counts, total_counts"> | |
58 <option value="n_cells_by_counts">n_cells_by_counts</option> | |
59 <option value="total_counts">total_counts</option> | |
60 </param> | |
61 <param name="min" type="float" value="-1e9" label="Min value"/> | |
62 <param name="max" type="float" value="1e9" label="Max value"/> | |
63 </repeat> | |
64 | |
65 <param name="cells_use" argument="--cells-use" type="data" format="txt" optional="true" | |
66 label="List of cells to include (optional)" | |
67 help="Text file with one cell per line providing cell names to use as a subset."/> | |
68 | |
69 <param name="cells_discard" argument="--cells-discard" type="data" format="txt" optional="true" | |
70 label="List of cells to exclude (optional)" | |
71 help="Text file with one cell per line providing cell names to discard as a subset."/> | |
72 | |
73 <param name="features_use" argument="--features-use" type="data" format="txt" optional="true" | |
74 label="List of features to include (optional)" | |
75 help="Text file with one features per line providing feature names to use as a subset."/> | |
76 | |
77 <param name="output_selected_cells" label="Output lists of pass-filter cells" type="boolean" checked="false"/> | |
78 | |
79 <param name="output_selected_features" label="Output lists of pass-filter features" type="boolean" checked="false"/> | |
80 | |
81 </inputs> | |
82 | |
83 <outputs> | |
84 <data name="R_scater_filtered" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object"/> | |
85 | |
86 <data name="selected_cells" format="tsv" label="${tool.name} on ${on_string}: pass-filter cells"> | |
87 <filter>output_selected_cells</filter> | |
88 </data> | |
89 <data name="selected_featuers" format="tsv" label="${tool.name} on ${on_string}: pass-filter features"> | |
90 <filter>output_selected_features</filter> | |
91 </data> | |
92 </outputs> | |
93 | |
94 <tests> | |
95 <test> | |
96 <param name="R_scater_qc" value="R_scater_qc.rds"/> | |
97 <output name="R_scater_filtered" file="R_scater_filtered.rds"/> | |
98 </test> | |
99 </tests> | |
100 | |
101 <help><![CDATA[ | |
102 @HELP@ | |
103 | |
104 @VERSION_HISTORY@ | |
105 ]]></help> | |
106 <expand macro="citations" /> | |
107 </tool> |