Mercurial > repos > ebi-gxa > anndata_ops

comparison anndata_operations.xml @ 30:a4774b7b2e85 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 16:42:14 +0000
parents 2e8022f1923c
children
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29:2e8022f1923c 30:a4774b7b2e85
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="anndata_ops" name="AnnData Operations" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@"> 2 <tool id="anndata_ops" name="AnnData Operations" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>modifies metadata and flags genes</description> 3 <description>is a Swiss army knife for AnnData files</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[
444 </outputs> 444 </outputs>
445 445
446 <tests> 446 <tests>
447 <test> 447 <test>
448 <param name="input_obj_file" value="find_cluster.h5"/> 448 <param name="input_obj_file" value="find_cluster.h5"/>
449 <output name="output_h5ad" file="anndata_ops.h5" ftype="h5ad" compare="sim_size"/> 449 <output name="output_h5ad" ftype="h5ad">
450 <assert_contents>
451 <has_h5_keys keys="var/gene_symbols"/>
452 </assert_contents>
453 </output>
450 </test> 454 </test>
451 <test> 455 <test>
452 <param name="input_obj_file" value="mnn.h5"/> 456 <param name="input_obj_file" value="mnn.h5"/>
453 <conditional name="swap_layer_to_x"> 457 <conditional name="swap_layer_to_x">
454 <param name="default" value="true"/> 458 <param name="default" value="true"/>
509 <param name="input_obj_file" value="find_cluster.h5"/> 513 <param name="input_obj_file" value="find_cluster.h5"/>
510 <conditional name="copy_r"> 514 <conditional name="copy_r">
511 <param name="default" value="true"/> 515 <param name="default" value="true"/>
512 <param name="r_source" value="read_10x.h5"/> 516 <param name="r_source" value="read_10x.h5"/>
513 </conditional> 517 </conditional>
514 <output name="output_h5ad" file="anndata_ops_raw.h5" ftype="h5ad" compare="sim_size"> 518 <output name="output_h5ad" ftype="h5ad">
515 <assert_contents> 519 <assert_contents>
516 <has_h5_keys keys="raw/X" /> 520 <has_h5_keys keys="raw/X" />
517 </assert_contents> 521 </assert_contents>
518 </output> 522 </output>
519 </test> 523 </test>
524 <repeat name="xlayers"> 528 <repeat name="xlayers">
525 <param name="x_source" value='filter_genes.h5'/> 529 <param name="x_source" value='filter_genes.h5'/>
526 <param name="dest" value='filtered'/> 530 <param name="dest" value='filtered'/>
527 </repeat> 531 </repeat>
528 </conditional> 532 </conditional>
529 <output name="output_h5ad" file="anndata_ops_xlayer.h5" ftype="h5ad" compare="sim_size"> 533 <output name="output_h5ad" ftype="h5ad">
530 <assert_contents> 534 <assert_contents>
531 <has_h5_keys keys="layers/filtered" /> 535 <has_h5_keys keys="layers/filtered" />
532 </assert_contents> 536 </assert_contents>
533 </output> 537 </output>
534 </test> 538 </test>
539 <repeat name="layers"> 543 <repeat name="layers">
540 <param name="contains" value='filtered'/> 544 <param name="contains" value='filtered'/>
541 </repeat> 545 </repeat>
542 <param name="layer_sources" value='anndata_ops_xlayer.h5'/> 546 <param name="layer_sources" value='anndata_ops_xlayer.h5'/>
543 </conditional> 547 </conditional>
544 <output name="output_h5ad" file="anndata_ops_layer.h5" ftype="h5ad" compare="sim_size"> 548 <output name="output_h5ad" ftype="h5ad">
545 <assert_contents> 549 <assert_contents>
546 <has_h5_keys keys="layers/filtered" /> 550 <has_h5_keys keys="layers/filtered" />
547 </assert_contents> 551 </assert_contents>
548 </output> 552 </output>
549 </test> 553 </test>