| Previous changeset 6:00712416fdaa (2020-07-22) Next changeset 8:ae1e5d9d8972 (2021-02-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a" |
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modified:
import.xml macros.xml test-data/inspect.general.txt test-data/manipulate.concatenate.h5ad |
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| diff -r 00712416fdaa -r cfc3f5a57dc6 import.xml --- a/import.xml Wed Jul 22 12:21:43 2020 -0400 +++ b/import.xml Thu Jan 07 23:28:53 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="anndata_import" name="Import Anndata and loom" version="@VERSION@+@GALAXY_VERSION@" profile="18.01"> +<tool id="anndata_import" name="Import Anndata and loom" version="@VERSION@+@GALAXY_VERSION@" profile="20.09"> <description>from different format</description> <macros> <import>macros.xml</import> @@ -58,7 +58,7 @@ <configfile name="script_file"><![CDATA[ @CMD_imports@ #if $hd5_format.filetype == 'anndata' -#if $hd5_format.in.adata_format == 'loom' + #if $hd5_format.in.adata_format == 'loom' adata = ad.read_loom( '$hd5_format.in.input', sparse=$hd5_format.in.sparse, @@ -67,24 +67,24 @@ obs_names='$hd5_format.in.obs_names', var_names='$hd5_format.in.var_names') -#else if $hd5_format.in.adata_format == 'tabular' - #set delimiter=$hd5_format.in.input.metadata.delimiter - #if $delimiter != ',' - #set delimiter='\\t' - #end if + #else if $hd5_format.in.adata_format == 'tabular' + #set delimiter=$hd5_format.in.input.metadata.delimiter + #if $delimiter != ',' + #set delimiter='\\t' + #end if adata = ad.read_csv( '$hd5_format.in.input', delimiter='$delimiter', first_column_names=$hd5_format.in.first_column_names) -#else if $hd5_format.in.adata_format == '10x_h5' + #else if $hd5_format.in.adata_format == '10x_h5' import scanpy as sc adata = sc.read_10x_h5('$hd5_format.in.input') -#else if $hd5_format.in.adata_format == 'mtx' - #if $hd5_format.in.tenx.use == 'no' + #else if $hd5_format.in.adata_format == 'mtx' + #if $hd5_format.in.tenx.use == 'no' adata = ad.read_mtx(filename='$hd5_format.in.matrix') - #else + #else import scanpy as sc adata = sc.read_10x_mtx( 'mtx', @@ -92,12 +92,11 @@ make_unique=$hd5_format.in.tenx.make_unique, cache=False, gex_only=$hd5_format.in.tenx.gex_only) - #end if + #end if -#else if $hd5_format.in.adata_format == 'umi_tools' + #else if $hd5_format.in.adata_format == 'umi_tools' adata = ad.read_umi_tools('${hd5_format.in.input}.gz') - -#end if + #end if adata.write('anndata.h5ad') #end if ]]></configfile> @@ -176,7 +175,7 @@ <test expect_num_outputs="1"> <conditional name="in"> <param name="adata_format" value="loom"/> - <param name="input" value="krumsiek11.loom" /> + <param name="input" ftype="loom" value="krumsiek11.loom" /> <param name="sparse" value="True"/> <param name="cleanup" value="False"/> <param name="x_name" value="spliced"/> @@ -219,7 +218,7 @@ </assert_stdout> <output name="anndata" value="import.tsv.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <!--<test expect_num_outputs="1"> + <test expect_num_outputs="1"> <conditional name="in"> <param name="adata_format" value="mtx"/> <param name="matrix" value="matrix_10x_v1.2.0.mtx"/> @@ -229,7 +228,7 @@ </conditional> <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/> </test> - <test> + <!--<test> <conditional name="in"> <param name="adata_format" value="mtx"/> <param name="matrix" value="matrix_10x_v1.2.0.mtx"/> @@ -293,6 +292,7 @@ </test> </tests> <help><![CDATA[ + **What it does** This tool creates an AnnData or loom dataset from several input types: |
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| diff -r 00712416fdaa -r cfc3f5a57dc6 macros.xml --- a/macros.xml Wed Jul 22 12:21:43 2020 -0400 +++ b/macros.xml Thu Jan 07 23:28:53 2021 +0000 |
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| @@ -1,6 +1,6 @@ <macros> - <token name="@VERSION@">0.6.22.post1</token> - <token name="@GALAXY_VERSION@">galaxy4</token> + <token name="@VERSION@">0.7.4</token> + <token name="@GALAXY_VERSION@">galaxy1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">anndata</requirement> |
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| diff -r 00712416fdaa -r cfc3f5a57dc6 test-data/inspect.general.txt --- a/test-data/inspect.general.txt Wed Jul 22 12:21:43 2020 -0400 +++ b/test-data/inspect.general.txt Thu Jan 07 23:28:53 2021 +0000 |
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| @@ -1,3 +1,3 @@ -AnnData object with n_obs × n_vars = 640 × 11 +AnnData object with n_obs × n_vars = 640 × 11 obs: 'cell_type' uns: 'cell_type_colors', 'highlights', 'iroot' |
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| diff -r 00712416fdaa -r cfc3f5a57dc6 test-data/manipulate.concatenate.h5ad |
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| Binary file test-data/manipulate.concatenate.h5ad has changed |