Mercurial > repos > iuc > scanpy_remove_confounders

comparison remove_confounders.xml @ 6:f2f6c703da06 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
author iuc
date Thu, 20 Feb 2020 08:24:15 -0500
parents 524aa62a6066
children 215733a383f2
comparison
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5:524aa62a6066 6:f2f6c703da06
101 </when> 101 </when>
102 <when value="pp.combat"> 102 <when value="pp.combat">
103 <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal"/> 103 <param argument="key" type="text" value="batch" label="Key to a categorical annotation from adata.obs that will be used for batch effect removal"/>
104 </when> 104 </when>
105 </conditional> 105 </conditional>
106 <expand macro="inputs_common_advanced"/>
106 </inputs> 107 </inputs>
107 <outputs> 108 <outputs>
108 <expand macro="anndata_outputs"/> 109 <expand macro="anndata_outputs"/>
109 </outputs> 110 </outputs>
110 <tests> 111 <tests>
111 <test> 112 <test>
112 <!-- test 1 --> 113 <!-- test 0 -->
113 <param name="adata" value="krumsiek11.h5ad" /> 114 <param name="adata" value="krumsiek11.h5ad" />
114 <conditional name="method"> 115 <conditional name="method">
115 <param name="method" value="pp.regress_out"/> 116 <param name="method" value="pp.regress_out"/>
116 <param name="keys" value="cell_type"/> 117 <param name="keys" value="cell_type"/>
117 </conditional> 118 </conditional>
118 <assert_stdout> 119 <section name="advanced_common">
119 <has_text_matching expression="sc.pp.regress_out"/> 120 <param name="show_log" value="true" />
120 <has_text_matching expression="keys=\['cell_type'\]"/> 121 </section>
121 </assert_stdout> 122 <output name="hidden_output">
123 <assert_contents>
124 <has_text_matching expression="sc.pp.regress_out"/>
125 <has_text_matching expression="keys=\['cell_type'\]"/>
126 </assert_contents>
127 </output>
122 <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 128 <output name="anndata_out" file="pp.regress_out.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
123 </test> 129 </test>
124 <!--<test> 130 <!--<test>
125 < test 2 > 131 < test 2 >
126 <param name="adata" value="krumsiek11.h5ad" /> 132 <param name="adata" value="krumsiek11.h5ad" />
133 <has_text_matching expression="keys='cell_type'"/> 139 <has_text_matching expression="keys='cell_type'"/>
134 </assert_stdout> 140 </assert_stdout>
135 <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 141 <output name="anndata_out" file="pp.mnn_correct.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
136 </test>--> 142 </test>-->
137 <test> 143 <test>
138 <!-- test 2 --> 144 <!-- test 1 -->
139 <param name="adata" value="blobs.h5ad" /> 145 <param name="adata" value="blobs.h5ad" />
140 <conditional name="method"> 146 <conditional name="method">
141 <param name="method" value="pp.combat"/> 147 <param name="method" value="pp.combat"/>
142 <param name="key" value="blobs"/> 148 <param name="key" value="blobs"/>
143 </conditional> 149 </conditional>
144 <assert_stdout> 150 <section name="advanced_common">
145 <has_text_matching expression="sc.pp.combat"/> 151 <param name="show_log" value="true" />
146 <has_text_matching expression="key='blobs'"/> 152 </section>
147 </assert_stdout> 153 <output name="hidden_output">
154 <assert_contents>
155 <has_text_matching expression="sc.pp.combat"/>
156 <has_text_matching expression="key='blobs'"/>
157 </assert_contents>
158 </output>
148 <output name="anndata_out" file="pp.combat.blobs.h5ad" ftype="h5ad" compare="sim_size"/> 159 <output name="anndata_out" file="pp.combat.blobs.h5ad" ftype="h5ad" compare="sim_size"/>
149 </test> 160 </test>
150 </tests> 161 </tests>
151 <help><![CDATA[ 162 <help><![CDATA[
152 Regress out unwanted sources of variation, using `pp.regress_out` 163 Regress out unwanted sources of variation, using `pp.regress_out`