Mercurial > repos > ebi-gxa > scanpy_filter_cells

annotate scanpy-filter-cells.xml @ 2:fd03785d0935 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3fc448754d6720855f781caa7938e33d3961b092"
author ebi-gxa
date Thu, 16 Apr 2020 09:03:54 +0000
parents 4c806f3f094c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
1 <?xml version="1.0" encoding="utf-8"?>
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
2 <tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@" >
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
3 <description>based on counts and numbers of genes expressed</description>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
4 <macros>
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
5 <import>scanpy_macros2.xml</import>
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
6 </macros>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
7 <expand macro="requirements"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
9 ln -s '${input_obj_file}' input.h5 &&
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
10 PYTHONIOENCODING=utf-8 scanpy-filter-cells
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
11 #if $gene_name
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
12 --gene-name '${gene_name}'
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
13 #end if
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
14 #if $parameters
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
15 #for $p in $parameters
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
16 #set $min = $p.min
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
17 #set $max = $p.max
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
18 #if $p.name.startswith('pct_')
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
19 #set $min = float($min) / 100
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
20 #set $max = float($max) / 100
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
21 #end if
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
22 --param 'c:$p.name' $min $max
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
23 #end for
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
24 #end if
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
25 #if $categories
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
26 #set cats = ' '.join(["--category 'c:{name}' '{negate}{values}'".format(**$c) for $c in $categories])
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
27 ${cats}
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
28 #end if
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
29 #if $subsets
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
30 #set subs = ' '.join(["--subset 'c:{name}' '{subset}'".format(**$s) for $s in $subsets])
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
31 ${subs}
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
32 #end if
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
33 @INPUT_OPTS@
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
34 @OUTPUT_OPTS@
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
35 @EXPORT_MTX_OPTS@
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
36 ]]></command>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
37
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
38 <inputs>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
39 <expand macro="input_object_params"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
40 <expand macro="output_object_params"/>
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
41
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
42 <param name="gene_name" type="text" optional="true" label="Name of the column in `anndata.var` that contains gene name"
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
43 help="Used for flagging mitochondria genes (starting with 'MT-'). Leave empty if gene table already has a boolean column called 'mito' that flags MT genes"/>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
44
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
45 <repeat name="parameters" title="Parameters to select cells to keep" min="1">
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
46 <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts">
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
47 <option value="n_genes">n_genes</option>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
48 <option value="n_counts">n_counts</option>
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
49 <option value="pct_counts_mito">pct_counts_mito (only usable if MT genes are flagged or has been pre-calculated)</option>
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
50 </param>
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
51 <param name="min" type="float" value="0" min="0" label="Min value" help="Cells with value below min will be discarded."/>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
52 <param name="max" type="float" value="1e9" label="Max value" help="Cells with value above max will be discarded."/>
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
53 </repeat>
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
54
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
55 <repeat name="categories" title="Categories to select cells to keep (unless negate is checked)" min="0">
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
56 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
57 <param name="values" type="text" value="" label="Comma-separated list of categories" help="Cells with these values in this categorical variable will be kept."/>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
58 <param name="negate" type="boolean" truevalue="!" falsevalue="" checked="false" label="Apply as negative filter" help="If enabled, specified categories will be removed rather than retained."/>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
59 </repeat>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
60
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
61 <repeat name="subsets" title="Subsets to select cells to keep" min="0">
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
62 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
63 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
64 </repeat>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
65 <param name="force_recalc" label="Force recalculation of QC vars" type="boolean" truevalue="--force-recalc" falsevalue="" help="If set, it will recalculate pcts and other existing QC vars, overwriting existing ones."/>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
66 <expand macro="export_mtx_params"/>
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
67 </inputs>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
68
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
69 <outputs>
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
70 <expand macro="output_data_obj" description="Filtered cells"/>
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
71 <expand macro="export_mtx_outputs"/>
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
72 </outputs>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
73
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
74 <tests>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
75 <test>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
76 <param name="input_obj_file" value="read_10x.h5"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
77 <param name="input_format" value="anndata"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
78 <param name="output_format" value="anndata"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
79 <repeat name="parameters">
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
80 <param name="name" value="n_genes"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
81 <param name="min" value="200"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
82 <param name="max" value="2500"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
83 </repeat>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
84 <repeat name="parameters">
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
85 <param name="name" value="n_counts"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
86 <param name="min" value="0"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
87 <param name="max" value="1e9"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
88 </repeat>
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
89 <output name="output_h5" file="output.h5" ftype="h5" compare="sim_size"/>
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
90 </test>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
91 </tests>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
92
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
93 <help><![CDATA[
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
94 ===================================================================
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
95 Filter cells based on various QC metrics (`scanpy.pp.filter_cells`)
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
96 ===================================================================
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
97
1
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
98 For instance, only keep cells with at least `min_counts` and at most
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
99 `max_counts` UMI and/or at least `min_genes` expressed genes and/or at most
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
100 `max_mito_percent` mitocondria expression. This is to filter measurement
4c806f3f094c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
ebi-gxa
parents: 0
diff changeset
101 outliers, i.e., "unreliable" observations.
0
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
102
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
103 @HELP@
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
104
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
105 @VERSION_HISTORY@
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
106 ]]></help>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
107 <expand macro="citations"/>
cad451be0a2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48
ebi-gxa
parents:
diff changeset
108 </tool>