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comparison scanpy-integrate-harmony.xml @ 14:c354af93f567 draft default tip

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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 ee197a80b2d591c393e1662854bc119b2ecab11e-dirty
author ebi-gxa
date Tue, 27 Feb 2024 16:43:15 +0000
parents 18e01a7c55c6
children
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13:18e01a7c55c6 14:c354af93f567
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@"> 2 <tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>adjust principal components for variables that might introduce batch effect</description> 3 <description>adjust principal components 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 '${input_obj_file}' input.h5 &&
11 PYTHONIOENCODING=utf-8 scanpy-integrate harmony 11 PYTHONIOENCODING=utf-8 scanpy-cli integrate harmony
12 --batch-key '${batch_key}' 12 --batch-key '${batch_key}'
13 #if $basis 13 #if $basis
14 --basis '${basis}' 14 --basis '${basis}'
15 #end if 15 #end if
16 --adjusted-basis '${adjusted_basis}' 16 --adjusted-basis '${adjusted_basis}'
112 <test> 112 <test>
113 <param name="input_obj_file" value="find_cluster.h5"/> 113 <param name="input_obj_file" value="find_cluster.h5"/>
114 <param name="input_format" value="anndata"/> 114 <param name="input_format" value="anndata"/>
115 <param name="output_format" value="anndata"/> 115 <param name="output_format" value="anndata"/>
116 <param name="batch_key" value="louvain"/> 116 <param name="batch_key" value="louvain"/>
117 <output name="output_h5" file="harmony.h5" ftype="h5" compare="sim_size"/> 117 <output name="output_h5" ftype="h5">
118 <assert_contents>
119 <has_h5_keys keys="obsm/X_pca_harmony"/>
120 </assert_contents>
121 </output>
118 </test> 122 </test>
119 <test> 123 <test>
120 <param name="input_obj_file" value="find_cluster.h5"/> 124 <param name="input_obj_file" value="find_cluster.h5"/>
121 <param name="input_format" value="anndata"/> 125 <param name="input_format" value="anndata"/>
122 <param name="output_format" value="anndata"/> 126 <param name="output_format" value="anndata"/>
123 <output name="output_h5" file="harmony_copy.h5" ftype="h5" compare="sim_size"/> 127 <output name="output_h5" file="harmony_copy.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
124 </test> 128 </test>
125 </tests> 129 </tests>
126 130
127 <help><![CDATA[ 131 <help><![CDATA[
128 .. class:: infomark 132 .. class:: infomark