Mercurial > repos > ebi-gxa > scanpy_find_cluster
comparison scanpy-find-cluster.xml @ 16:5e68e130fafe draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"
author | ebi-gxa |
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date | Thu, 17 Sep 2020 16:24:22 +0000 |
parents | c46750e2e4a4 |
children | b45b85d5c7ec |
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15:ed07813a7266 | 16:5e68e130fafe |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> | 2 <tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
3 <description>based on community detection on KNN graph</description> | 3 <description>based on community detection on KNN graph</description> |
4 <macros> | 4 <macros> |
5 <import>scanpy_macros2.xml</import> | 5 <import>scanpy_macros2.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 #from pathlib import Path | |
10 #if $settings.resolution_file | |
11 #set resolution = Path($settings.resolution_file.__str__).read_text().strip() | |
12 #elif $settings.resolution | |
13 #set resolution = $settings.resolution.__str__.strip() | |
14 #end if | |
15 | |
9 ln -s '${input_obj_file}' input.h5 && | 16 ln -s '${input_obj_file}' input.h5 && |
10 PYTHONIOENCODING=utf-8 scanpy-find-cluster | 17 PYTHONIOENCODING=utf-8 scanpy-find-cluster |
11 ${method} | 18 ${method} |
12 #if $settings.default == "false" | 19 #if $settings.default == "false" |
13 --neighbors-key '${settings.neighbors_key}' | 20 --neighbors-key '${settings.neighbors_key}' |
21 #if $settings.key_added | |
22 #set key_added = $settings.key_added.replace('METHOD', $method.__str__) | |
23 #if $resolution | |
24 #set key_added = $key_added.replace('RESOLUTION', $resolution.__str__) | |
25 #end if | |
26 --key-added '${key_added}' | |
27 #end if | |
28 #if $resolution | |
29 --resolution '$resolution' | |
30 #end if | |
14 #if $settings.layer | 31 #if $settings.layer |
15 --layer '${settings.layer}' | 32 --layer '${settings.layer}' |
16 #end if | |
17 #if $settings.key_added | |
18 --key-added '${settings.key_added}' | |
19 #end if | |
20 #if $settings.resolution_file | |
21 --resolution \$( cat $settings.resolution_file ) | |
22 #elif $settings.resolution | |
23 --resolution '${settings.resolution}' | |
24 #end if | 33 #end if |
25 #if $settings.restrict_to | 34 #if $settings.restrict_to |
26 --restrict-to '${settings.restrict_to}' | 35 --restrict-to '${settings.restrict_to}' |
27 #end if | 36 #end if |
28 #if $settings.use_weights | 37 #if $settings.use_weights |
55 <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text" | 64 <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text" |
56 label="Name of the slot that holds the KNN graph"/> | 65 label="Name of the slot that holds the KNN graph"/> |
57 <param name="layer" argument="--layer" value="" type="text" | 66 <param name="layer" argument="--layer" value="" type="text" |
58 label="Key from adata.layers whose value will be used to perform tests on. (Default: use .X)"/> | 67 label="Key from adata.layers whose value will be used to perform tests on. (Default: use .X)"/> |
59 <param name="key_added" argument="--key-added" type="text" optional="true" | 68 <param name="key_added" argument="--key-added" type="text" optional="true" |
60 label="Additional suffix to the name of the slot to save the calculated clustering"/> | 69 label="Additional suffix to the name of the slot to save the calculated clustering" help="If included, the keyword 'METHOD' will be substituted with the value of the method setting and 'RESOLUTION' with the value of that field."/> |
61 | |
62 <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0" | 70 <param name="resolution" argument="--resolution" type="float" min="0.0" value="1.0" |
63 label="Resolution, high value for more and smaller clusters"/> | 71 label="Resolution, high value for more and smaller clusters"/> |
64 <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true" | 72 <param name="resolution_file" argument="--resolution" type="data" format="txt,tsv" optional="true" |
65 label="File with resolution, use with parameter iterator. Overrides the resolution setting"/> | 73 label="File with resolution, use with parameter iterator. Overrides the resolution setting"/> |
66 <param name="restrict_to" argument="--restrict-to" type="text" optional="true" | 74 <param name="restrict_to" argument="--restrict-to" type="text" optional="true" |