Mercurial > repos > iuc > anndata_manipulate

comparison manipulate.xml @ 16:e0161aea7682 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata commit 7511ac8af2d638d0ad54f196b5ab3657c7577aa5
author iuc
date Wed, 10 Dec 2025 16:59:25 +0000
parents 9402539a3aea
children
comparison
equal deleted inserted replaced
15:b06f3ed7b60b 16:e0161aea7682
83 adata.obs = adata.obs.drop(columns=$keys) 83 adata.obs = adata.obs.drop(columns=$keys)
84 #end if 84 #end if
85 85
86 #if $manipulate.var_keys 86 #if $manipulate.var_keys
87 #set $keys = [x.strip() for x in str($manipulate.var_keys).split(',')] 87 #set $keys = [x.strip() for x in str($manipulate.var_keys).split(',')]
88 adata.var = adata.vars.drop(columns=$keys) 88 adata.var = adata.var.drop(columns=$keys)
89 #end if 89 #end if
90 90
91 #else if $manipulate.function == 'flag_genes' 91 #else if $manipulate.function == 'flag_genes'
92 ## adapted from anndata operations 92 ## adapted from anndata operations
93 #for $flag in $manipulate.gene_flags 93 #for $flag in $manipulate.gene_flags
588 </assert_contents> 588 </assert_contents>
589 </output> 589 </output>
590 </test> 590 </test>
591 <test expect_num_outputs="1"> 591 <test expect_num_outputs="1">
592 <!-- test 10 remove_keys --> 592 <!-- test 10 remove_keys -->
593 <param name="input" value="krumsiek11.h5ad"/> 593 <param name="input" value="flagged.h5ad"/>
594 <conditional name="manipulate"> 594 <conditional name="manipulate">
595 <param name="function" value="remove_keys"/> 595 <param name="function" value="remove_keys"/>
596 <param name="obs_keys" value="cell_type"/> 596 <param name="obs_keys" value="cell_type"/>
597 </conditional> 597 <param name="var_keys" value="GF"/>
598 <assert_stdout> 598 </conditional>
599 <has_text_matching expression="500 × 11"/> 599 <assert_stdout>
600 </assert_stdout> 600 <has_text_matching expression="500 × 11"/>
601 <output name="anndata" ftype="h5ad"> 601 </assert_stdout>
602 <assert_contents> 602 <output name="anndata" ftype="h5ad">
603 <has_h5_keys keys="uns/highlights"/> 603 <assert_contents>
604 <has_h5_keys keys="uns/iroot"/> 604 <has_h5_keys keys="uns/highlights"/>
605 <has_h5_keys keys="uns/iroot"/>
606 <has_h5_keys keys="var/Gata_TF"/>
605 </assert_contents> 607 </assert_contents>
606 </output> 608 </output>
607 </test> 609 </test>
608 <test expect_num_outputs="1"> 610 <test expect_num_outputs="1">
609 <!-- test 11 flag_genes --> 611 <!-- test 11 flag_genes -->