Mercurial > repos > ebi-gxa > scanpy_integrate_combat

comparison scanpy-integrate-combat.xml @ 15:3c47bc560688 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 ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:23 +0000
parents c6611adc8f4a
children
comparison
equal deleted inserted replaced
14:c6611adc8f4a 15:3c47bc560688
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@"> 2 <tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>adjust expression for variables that might introduce batch effect</description> 3 <description>adjust expression for variables that might introduce batch effect</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 #if $batch_key 9 #if $batch_key
10 ln -s '${input_obj_file}' input.h5 && 10 ln -s '${input_obj_file}' input.h5 &&
11 PYTHONIOENCODING=utf-8 scanpy-integrate combat 11 PYTHONIOENCODING=utf-8 scanpy-cli integrate combat
12 --batch-key '${batch_key}' 12 --batch-key '${batch_key}'
13 #if $batch_layer 13 #if $batch_layer
14 --batch-layer '${batch_layer}' 14 --batch-layer '${batch_layer}'
15 #end if 15 #end if
16 #if $covariates 16 #if $covariates
56 <test> 56 <test>
57 <param name="input_obj_file" value="find_cluster.h5"/> 57 <param name="input_obj_file" value="find_cluster.h5"/>
58 <param name="input_format" value="anndata"/> 58 <param name="input_format" value="anndata"/>
59 <param name="output_format" value="anndata"/> 59 <param name="output_format" value="anndata"/>
60 <param name="batch_key" value="louvain"/> 60 <param name="batch_key" value="louvain"/>
61 <output name="output_h5" file="combat.h5" ftype="h5" compare="sim_size"/> 61 <output name="output_h5" ftype="h5">
62 <assert_contents>
63 <has_h5_keys keys="layers/combat"/>
64 </assert_contents>
65 </output>
62 </test> 66 </test>
63 <test> 67 <test>
64 <param name="input_obj_file" value="find_cluster.h5"/> 68 <param name="input_obj_file" value="find_cluster.h5"/>
65 <param name="input_format" value="anndata"/> 69 <param name="input_format" value="anndata"/>
66 <param name="output_format" value="anndata"/> 70 <param name="output_format" value="anndata"/>
67 <output name="output_h5" file="combat_copy.h5" ftype="h5" compare="sim_size"/> 71 <output name="output_h5" file="combat_copy.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
68 </test> 72 </test>
69 </tests> 73 </tests>
70 74
71 <help><![CDATA[ 75 <help><![CDATA[
72 .. class:: infomark 76 .. class:: infomark