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comparison scanpy-run-dpt.xml @ 12:820493156c4a draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 13:10:11 +0000
parents 0e264c40fd06
children 2e06dabb3f2f
comparison
equal deleted inserted replaced
11:1ab80fc6f667 12:820493156c4a
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@"> 2 <tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>diffusion pseudotime inference</description> 3 <description>diffusion pseudotime inference</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"/>
13 #if $n_branchings > 0 13 #if $n_branchings > 0
14 --n-branchings ${n_branchings} 14 --n-branchings ${n_branchings}
15 --min-group-size ${min_group_size} 15 --min-group-size ${min_group_size}
16 #end if 16 #end if
17 #if $use_graph 17 #if $use_graph
18 --use-graph '${use_graph}' 18 --neighbors-key '${use_graph}'
19 #end if 19 #end if
20 #if $key_added 20 #if $key_added
21 --key-added '${key_added}' 21 --key-added '${key_added}'
22 #end if
23 #if not $allow_kendall_tau_shift
24 --disallow-kendall-tau-shift
22 #end if 25 #end if
23 @INPUT_OPTS@ 26 @INPUT_OPTS@
24 @OUTPUT_OPTS@ 27 @OUTPUT_OPTS@
25 ]]></command> 28 ]]></command>
26 29
37 help="Ignored when `Number of branchings to detect` is 0"/> 40 help="Ignored when `Number of branchings to detect` is 0"/>
38 <param name="root_attr" argument="--root {attr} value" type="text" 41 <param name="root_attr" argument="--root {attr} value" type="text"
39 label="Name of attribute that defines clustering"/> 42 label="Name of attribute that defines clustering"/>
40 <param name="root_value" argument="--root attr {value}" type="text" 43 <param name="root_value" argument="--root attr {value}" type="text"
41 label="Name of the clustering that defines the root cell type"/> 44 label="Name of the clustering that defines the root cell type"/>
42 <param name="use_graph" argument="--use-graph" value="neighbors" type="text" 45 <param name="use_graph" argument="--neighbors-key" value="neighbors" type="text"
43 label="Name of the slot that holds the KNN graph"/> 46 label="Name of the slot that holds the KNN graph"/>
44 <param name="key_added" argument="--key-added" type="text" optional="true" 47 <param name="key_added" argument="--key-added" type="text" optional="true"
45 label="Additional suffix to the name of the slot to save the calculated pseudo-time"/> 48 label="Additional suffix to the name of the slot to save the calculated pseudo-time"/>
49 <param name="allow_kendall_tau_shift" type="boolean" checked="true" label="Allow Kendall Tau shift" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of [Haghverdi16] to stabilize the splitting" />
46 </inputs> 50 </inputs>
47 51
48 <outputs> 52 <outputs>
49 <expand macro="output_data_obj" description="Diffussion pseudotime inference"/> 53 <expand macro="output_data_obj" description="Diffussion pseudotime inference"/>
50 </outputs> 54 </outputs>
53 <test> 57 <test>
54 <param name="input_obj_file" value="diffmap.h5"/> 58 <param name="input_obj_file" value="diffmap.h5"/>
55 <param name="input_format" value="anndata"/> 59 <param name="input_format" value="anndata"/>
56 <param name="output_format" value="anndata"/> 60 <param name="output_format" value="anndata"/>
57 <param name="n_dcs" value="10"/> 61 <param name="n_dcs" value="10"/>
58 <param name="root_attr" value="leiden"/> 62 <param name="root_attr" value="louvain"/>
59 <param name="root_value" value="1"/> 63 <param name="root_value" value="1"/>
60 <param name="use_graph" value="neighbors"/> 64 <param name="use_graph" value="neighbors"/>
61 <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/> 65 <output name="output_h5" file="dpt.h5" ftype="h5" compare="sim_size"/>
62 </test> 66 </test>
63 </tests> 67 </tests>
64 68
65 <help><![CDATA[ 69 <help><![CDATA[
66 ================================================ 70 ================================================