| Previous changeset 20:64388be6d510 (2024-10-18) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 637a6ebb9ca7f745c83146151cb1655cc902afc6 |
|
modified:
filter.xml |
| b |
| diff -r 64388be6d510 -r 5b3c1679d29b filter.xml --- a/filter.xml Fri Oct 18 10:35:58 2024 +0000 +++ b/filter.xml Thu Jan 09 15:54:14 2025 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="scanpy_filter" name="Scanpy filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+<tool id="scanpy_filter" name="Scanpy filter" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">\n <description>mark and subsample</description>\n <macros>\n <import>macros.xml</import>\n@@ -49,6 +49,58 @@\n \n @CMD_ANNDATA_WRITE_OUTPUTS@\n \n+#else if $method.method == \'filter_any\'\n+ #if $method.filter.filter == \'key\'\n+ #if $method.var_obs == \'var\'\n+filtered = adata.var[\'$method.filter.key\']\n+ #else if $method.var_obs == \'obs\'\n+filtered = adata.obs[\'$method.filter.key\']\n+ #end if\n+\n+ #if $method.filter.filter_key.type == \'number\'\n+ #if $method.filter.filter_key.filter == \'equal\'\n+filtered = filtered == $method.filter.filter_key.value\n+ #else if $method.filter.filter_key.filter == \'equal\'\n+filtered = filtered != $method.filter.filter_key.value\n+ #else if $method.filter.filter_key.filter == \'less\'\n+filtered = filtered < $method.filter.filter_key.value\n+ #else if $method.filter.filter_key.filter == \'less_or_equal\'\n+filtered = filtered <= $method.filter.filter_key.value\n+ #else if $method.filter.filter_key.filter == \'greater\'\n+filtered = filtered > $method.filter.filter_key.value\n+ #else if $method.filter.filter_key.filter == \'greater_or_equal\'\n+filtered = filtered >= $method.filter.filter_key.value\n+ #end if\n+ #else if $method.filter.filter_key.type == \'text\'\n+ #if $method.filter.filter_key.filter == \'equal\'\n+filtered = filtered == \'$method.filter.filter_key.value\'\n+ #else\n+filtered = filtered != \'$method.filter.filter_key.value\'\n+ #end if\n+ #else if $method.filter.filter_key.type == \'boolean\'\n+filtered = filtered == $method.filter.filter_key.value\n+ #end if\n+\n+ #else if $method.filter.filter == \'index\'\n+ #if str($method.filter.index.format) == \'file\'\n+with open(\'$method.filter.index.file\', \'r\') as filter_f:\n+ filters = [str(x.strip()) for x in filter_f.readlines()]\n+filtered = filters\n+ #else\n+ #set $filters = [str(x.strip()) for x in $method.filter.index.text.split(\',\')]\n+filtered = $filters\n+ #end if\n+ #end if\n+print(filtered)\n+\n+ #if $method.var_obs == \'var\'\n+adata = adata[:,filtered]\n+ #else if $method.var_obs == \'obs\'\n+adata = adata[filtered, :]\n+ #end if\n+\n+@CMD_ANNDATA_WRITE_OUTPUTS@\n+\n #else if $method.method == \'tl.filter_rank_genes_groups\'\n sc.tl.filter_rank_genes_groups(\n adata,\n@@ -218,6 +270,7 @@\n <param argument="method" type="select" label="Method used for filtering">\n <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using \'pp.filter_cells\'</option>\n <option value="pp.filter_genes">Filter genes based on number of cells or counts, using \'pp.filter_genes\'</option>\n+ <option value="filter_any">Filter on any column of observations or variables</option>\n <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using \'tl.filter_rank_genes_groups\'</option>\n <option value="pp.highly_variable_genes">Annotate (and filter) highly variable genes, using \'pp.highly_variable_genes\'</option>\n <option value="pp.subsample">Subsample to a fraction of the number of observations, using \'pp.subsample\'</option>\n@@ -234,16 +287,16 @@\n <option value="max_genes">Maximum number of genes expressed</option>\n </param>\n <when value="min_counts">\n- <param argument="min_counts" type="integer" min="0" value="" label="Minimum number of counts required for a cell to pass filtering"/>\n+ <param argument="min_counts" type="i'..b' <output name="anndata_out" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="obs/cell_type"/>\n+ <has_h5_keys keys="uns/highlights"/>\n+ <has_h5_keys keys="uns/iroot"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <!-- test 5 -->\n+ <param name="adata" value="krumsiek11.h5ad"/>\n+ <conditional name="method">\n+ <param name="method" value="filter_any"/>\n+ <param name="var_obs" value="obs"/>\n+ <conditional name="filter">\n+ <param name="filter" value="key"/>\n+ <param name="key" value="cell_type"/>\n+ <conditional name="filter_key">\n+ <param name="type" value="text"/>\n+ <param name="filter" value="equal"/>\n+ <param name="value" value="progenitor"/>\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="320 \xc3\x97 11"/>\n+ </assert_stdout>\n+ <output name="anndata_out" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="obs/cell_type"/>\n+ <has_h5_keys keys="uns/highlights"/>\n+ <has_h5_keys keys="uns/iroot"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ <!-- test 6 -->\n <!-- Fails to write to anndata after tl.filter_rank_genes_groups\n Issue has been reported here: https://github.com/scverse/anndata/issues/726\n The current fix is: del adata.uns[\'rank_genes_groups_filtered\'] -->\n@@ -511,7 +673,7 @@\n </output>\n </test>\n \n- <!-- test 5 -->\n+ <!-- test 7 -->\n <test expect_num_outputs="2">\n <param name="adata" value="blobs.h5ad"/>\n <conditional name="method">\n@@ -539,7 +701,7 @@\n </output>\n </test>\n \n- <!-- test 6 -->\n+ <!-- test 8 -->\n <test expect_num_outputs="2">\n <param name="adata" value="krumsiek11.h5ad"/>\n <conditional name="method">\n@@ -570,7 +732,7 @@\n </output>\n </test>\n \n- <!-- test 7 -->\n+ <!-- test 9 -->\n <test expect_num_outputs="2">\n <param name="adata" value="krumsiek11.h5ad"/>\n <conditional name="method">\n@@ -600,8 +762,8 @@\n </output>\n </test>\n \n- <!-- test 8 -->\n- <test expect_num_outputs="2"> \n+ <!-- test 10 -->\n+ <test expect_num_outputs="2">\n <param name="adata" value="krumsiek11.h5ad"/>\n <conditional name="method">\n <param name="method" value="pp.subsample"/>\n@@ -630,7 +792,7 @@\n </output>\n </test>\n \n- <!-- test 9 -->\n+ <!-- test 11 -->\n <test expect_num_outputs="2">\n <param name="adata" value="random-randint.h5ad"/>\n <conditional name="method">\n@@ -657,7 +819,7 @@\n </output>\n </test>\n \n- <!-- test 10 -->\n+ <!-- test 12 -->\n <test expect_num_outputs="2">\n <param name="adata" value="random-randint.h5ad"/>\n <conditional name="method">\n@@ -686,7 +848,7 @@\n </output>\n </test>\n \n- <!-- test 10 -->\n+ <!-- test 13 -->\n <test expect_num_outputs="2">\n <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad"/>\n <conditional name="method">\n@@ -716,7 +878,7 @@\n </output>\n </test>\n \n- <!-- test 11 -->\n+ <!-- test 14 -->\n <test expect_num_outputs="2">\n <param name="adata" value="krumsiek11.h5ad"/>\n <conditional name="method">\n' |