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comparison inspect.xml @ 15:b6035c5e7e12 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
author iuc
date Thu, 19 Sep 2024 06:40:16 +0000
parents 1c36180febfb
children 6551272ddc04
comparison
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14:1c36180febfb 15:b6035c5e7e12
1 <tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 <xml name="params_score_genes"> 4 <xml name="params_score_genes">
5 <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling"/> 5 <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling"/>
6 <param argument="random_state" type="integer" value="0" label="Random seed for sampling"/> 6 <param argument="random_state" type="integer" value="0" label="Random seed for sampling"/>
144 groupby='$method.groupby', 144 groupby='$method.groupby',
145 #end if 145 #end if
146 use_raw=$method.use_raw, 146 use_raw=$method.use_raw,
147 #if str($method.groups) != '': 147 #if str($method.groups) != '':
148 #set $group=[x.strip() for x in str($method.groups).split(',')] 148 #set $group=[x.strip() for x in str($method.groups).split(',')]
149 groups='$group', 149 groups=$group,
150 #end if 150 #end if
151 #if str($method.layer) != '': 151 #if str($method.layer) != '':
152 layer='$method.layer', 152 layer='$method.layer',
153 #end if 153 #end if
154 #if str($method.ref.rest) == 'rest': 154 #if str($method.ref.rest) == 'rest':
444 <when value="lbfgs"> 444 <when value="lbfgs">
445 <param name="penalty" type="boolean" truevalue="l2" falsevalue="None" checked="true" label="use l2 penalty?"/> 445 <param name="penalty" type="boolean" truevalue="l2" falsevalue="None" checked="true" label="use l2 penalty?"/>
446 <expand macro="fit_intercept"/> 446 <expand macro="fit_intercept"/>
447 <expand macro="max_iter"/> 447 <expand macro="max_iter"/>
448 <expand macro="multi_class"/> 448 <expand macro="multi_class"/>
449 </when> 449 </when>
450 <when value="newton-cg"> 450 <when value="newton-cg">
451 <param name="penalty" type="boolean" truevalue="l2" falsevalue="None" checked="true" label="use l2 penalty?"/> 451 <param name="penalty" type="boolean" truevalue="l2" falsevalue="None" checked="true" label="use l2 penalty?"/>
452 <expand macro="fit_intercept"/> 452 <expand macro="fit_intercept"/>
453 <expand macro="max_iter"/> 453 <expand macro="max_iter"/>
454 <expand macro="multi_class"/> 454 <expand macro="multi_class"/>
558 </inputs> 558 </inputs>
559 <outputs> 559 <outputs>
560 <expand macro="anndata_outputs"/> 560 <expand macro="anndata_outputs"/>
561 </outputs> 561 </outputs>
562 <tests> 562 <tests>
563 563 <!-- test 1 -->
564 <!-- test 1 -->
565 <test expect_num_outputs="2"> 564 <test expect_num_outputs="2">
566 <param name="adata" value="sparce_csr_matrix.h5ad"/> 565 <param name="adata" value="sparce_csr_matrix.h5ad"/>
567 <conditional name="method"> 566 <conditional name="method">
568 <param name="method" value="pp.calculate_qc_metrics"/> 567 <param name="method" value="pp.calculate_qc_metrics"/>
569 <param name="qc_vars" value="mito,negative"/> 568 <param name="qc_vars" value="mito,negative"/>
612 <has_h5_keys keys="obs/n_genes_by_counts,obs/log1p_n_genes_by_counts,obs/total_counts,obs/log1p_total_counts,obs/pct_counts_in_top_50_genes,obs/pct_counts_in_top_100_genes,obs/pct_counts_in_top_200_genes,obs/pct_counts_in_top_300_genes,obs/total_counts_mito,obs/log1p_total_counts_mito,obs/pct_counts_mito,obs/total_counts_negative,obs/log1p_total_counts_negative,obs/pct_counts_negative"/> 611 <has_h5_keys keys="obs/n_genes_by_counts,obs/log1p_n_genes_by_counts,obs/total_counts,obs/log1p_total_counts,obs/pct_counts_in_top_50_genes,obs/pct_counts_in_top_100_genes,obs/pct_counts_in_top_200_genes,obs/pct_counts_in_top_300_genes,obs/total_counts_mito,obs/log1p_total_counts_mito,obs/pct_counts_mito,obs/total_counts_negative,obs/log1p_total_counts_negative,obs/pct_counts_negative"/>
613 <has_h5_keys keys="var/mito,var/negative,var/n_cells_by_counts,var/mean_counts,var/log1p_mean_counts,var/pct_dropout_by_counts,var/total_counts,var/log1p_total_counts"/> 612 <has_h5_keys keys="var/mito,var/negative,var/n_cells_by_counts,var/mean_counts,var/log1p_mean_counts,var/pct_dropout_by_counts,var/total_counts,var/log1p_total_counts"/>
614 </assert_contents> 613 </assert_contents>
615 </output> 614 </output>
616 </test> 615 </test>
617 616
618 <!-- test 3 --> 617 <!-- test 3 -->
619 <test expect_num_outputs="2"> 618 <test expect_num_outputs="2">
620 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad"/> 619 <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad"/>
621 <conditional name="method"> 620 <conditional name="method">
622 <param name="method" value="pp.neighbors"/> 621 <param name="method" value="pp.neighbors"/>
849 <output name="anndata_out" ftype="h5ad"> 848 <output name="anndata_out" ftype="h5ad">
850 <assert_contents> 849 <assert_contents>
851 <has_h5_keys keys="uns/rank_genes_groups"/> 850 <has_h5_keys keys="uns/rank_genes_groups"/>
852 </assert_contents> 851 </assert_contents>
853 </output> 852 </output>
854 </test> 853 </test>
855 854
856 <!-- test 10 --> 855 <!-- test 10 -->
856 <test expect_num_outputs="2">
857 <param name="adata" value="krumsiek11.h5ad"/>
858 <conditional name="method">
859 <param name="method" value="tl.rank_genes_groups"/>
860 <param name="groupby" value="cell_type"/>
861 <param name="groups" value="Ery"/>
862 <conditional name="ref">
863 <param name="rest" value="group_id"/>
864 <param name="reference" value="Mk"/>
865 </conditional>
866 <param name="n_genes" value="100"/>
867 <conditional name="tl_rank_genes_groups_method">
868 <param name="method" value="logreg"/>
869 <conditional name="solver">
870 <param name="solver" value="liblinear"/>
871 <conditional name="penalty">
872 <param name="penalty" value="l2"/>
873 <param name="random_state" value="1"/>
874 </conditional>
875 </conditional>
876 </conditional>
877 </conditional>
878 <section name="advanced_common">
879 <param name="show_log" value="true"/>
880 </section>
881 <output name="hidden_output">
882 <assert_contents>
883 <has_text_matching expression="sc.tl.rank_genes_groups"/>
884 <has_text_matching expression="groupby='cell_type'"/>
885 <has_text_matching expression="use_raw=False"/>
886 <has_text_matching expression="n_genes=100"/>
887 <has_text_matching expression="method='logreg'"/>
888 <has_text_matching expression="solver='liblinear'"/>
889 <has_text_matching expression="penalty='l2'"/>
890 <has_text_matching expression="dual=False"/>
891 <has_text_matching expression="fit_intercept=True"/>
892 <has_text_matching expression="intercept_scaling=1.0"/>
893 <has_text_matching expression="tol=0.0001"/>
894 <has_text_matching expression="C=1.0"/>
895 <has_text_matching expression="groups=\['Ery'\]"/>
896 <has_text_matching expression="reference='Mk'"/>
897 </assert_contents>
898 </output>
899 <output name="anndata_out" ftype="h5ad">
900 <assert_contents>
901 <has_h5_keys keys="uns/rank_genes_groups"/>
902 </assert_contents>
903 </output>
904 </test>
905
906 <!-- test 11 -->
857 <test expect_num_outputs="2"> 907 <test expect_num_outputs="2">
858 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad"/> 908 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad"/>
859 <conditional name="method"> 909 <conditional name="method">
860 <param name="method" value="tl.marker_gene_overlap"/> 910 <param name="method" value="tl.marker_gene_overlap"/>
861 <repeat name="reference_markers"> 911 <repeat name="reference_markers">
887 <has_h5_keys keys="uns/rank_genes_groups"/> 937 <has_h5_keys keys="uns/rank_genes_groups"/>
888 </assert_contents> 938 </assert_contents>
889 </output> 939 </output>
890 </test> 940 </test>
891 941
892 <!-- test 11 --> 942 <!-- test 12 -->
893 <test expect_num_outputs="2"> 943 <test expect_num_outputs="2">
894 <param name="adata" value="krumsiek11.h5ad"/> 944 <param name="adata" value="krumsiek11.h5ad"/>
895 <conditional name="method"> 945 <conditional name="method">
896 <param name="method" value="pp.log1p"/> 946 <param name="method" value="pp.log1p"/>
897 </conditional> 947 </conditional>
908 <has_h5_keys keys="uns/log1p"/> 958 <has_h5_keys keys="uns/log1p"/>
909 </assert_contents> 959 </assert_contents>
910 </output> 960 </output>
911 </test> 961 </test>
912 962
913 <!-- test 12 --> 963 <!-- test 13 -->
914 <test expect_num_outputs="2"> 964 <test expect_num_outputs="2">
915 <param name="adata" value="krumsiek11.h5ad"/> 965 <param name="adata" value="krumsiek11.h5ad"/>
916 <conditional name="method"> 966 <conditional name="method">
917 <param name="method" value="pp.scale"/> 967 <param name="method" value="pp.scale"/>
918 </conditional> 968 </conditional>
927 </output> 977 </output>
928 <output name="anndata_out" ftype="h5ad"> 978 <output name="anndata_out" ftype="h5ad">
929 <assert_contents> 979 <assert_contents>
930 <has_h5_keys keys="var/mean,var/std"/> 980 <has_h5_keys keys="var/mean,var/std"/>
931 </assert_contents> 981 </assert_contents>
932 </output> </test> 982 </output>
933 983 </test>
934 <!-- test 13 --> 984
985 <!-- test 14 -->
935 <test expect_num_outputs="2"> 986 <test expect_num_outputs="2">
936 <param name="adata" value="krumsiek11.h5ad"/> 987 <param name="adata" value="krumsiek11.h5ad"/>
937 <conditional name="method"> 988 <conditional name="method">
938 <param name="method" value="pp.scale"/> 989 <param name="method" value="pp.scale"/>
939 <param name="max_value" value="10"/> 990 <param name="max_value" value="10"/>
953 <has_h5_keys keys="var/mean,var/std"/> 1004 <has_h5_keys keys="var/mean,var/std"/>
954 </assert_contents> 1005 </assert_contents>
955 </output> 1006 </output>
956 </test> 1007 </test>
957 1008
958 <!-- test 14 --> 1009 <!-- test 15 -->
959 <test expect_num_outputs="2"> 1010 <test expect_num_outputs="2">
960 <param name="adata" value="random-randint.h5ad"/> 1011 <param name="adata" value="random-randint.h5ad"/>
961 <conditional name="method"> 1012 <conditional name="method">
962 <param name="method" value="pp.sqrt"/> 1013 <param name="method" value="pp.sqrt"/>
963 </conditional> 1014 </conditional>