| Previous changeset 4:080eab96d846 (2020-01-18) Next changeset 6:00712416fdaa (2020-07-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064" |
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modified:
import.xml macros.xml |
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added:
test-data/dropletutils_input.h5 |
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| diff -r 080eab96d846 -r 32e547223c9e import.xml --- a/import.xml Sat Jan 18 03:36:57 2020 -0500 +++ b/import.xml Wed Feb 05 19:20:12 2020 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="anndata_import" name="Import Anndata and loom" version="@VERSION@+@GALAXY_VERSION@"> +<tool id="anndata_import" name="Import Anndata and loom" version="@VERSION@+@GALAXY_VERSION@" profile="18.01"> <description>from different format</description> <macros> <import>macros.xml</import> @@ -77,6 +77,10 @@ delimiter='$delimiter', first_column_names=$hd5_format.in.first_column_names) +#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 $hd5_format.in.tenx.use == 'no' adata = ad.read_mtx(filename='$hd5_format.in.matrix') @@ -109,6 +113,7 @@ <param name="adata_format" type="select" label="Format for the annotated data matrix"> <option value="loom">Loom</option> <option value="tabular">Tabular, CSV, TSV</option> + <option value="10x_h5">H5 format from Cell ranger or not</option> <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option> <option value="umi_tools">UMI tools</option> </param> @@ -124,6 +129,9 @@ <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/> <param name="first_column_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Does the first column store the row names?"/> </when> + <when value="10x_h5" > + <param name="input" type="data" format="h5" label="Data matrix"/> + </when> <when value="mtx"> <param name="matrix" type="data" format="mtx" label="Matrix"/> <conditional name="tenx"> @@ -267,6 +275,22 @@ <param name="rowdata" value="rows.tsv"/> <output name="loomdata" value="converted.loom.test" ftype="loom" compare="sim_size"/> </test> + <test expect_num_outputs="1"><!-- 10x h5 test --> + <conditional name="hd5_format"> + <param name="filetype" value="anndata"/> + <conditional name="in"> + <param name="adata_format" value="10x_h5"/> + <param name="input" value="dropletutils_input.h5"/> + </conditional> + </conditional> + <output name="anndata"> + <assert_contents> + <has_text text="HDF"/> + <has_text text="ENSG00000258728" /> + <has_text text="GCGAGAAAGTTGTAGA" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ **What it does** |
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| diff -r 080eab96d846 -r 32e547223c9e macros.xml --- a/macros.xml Sat Jan 18 03:36:57 2020 -0500 +++ b/macros.xml Wed Feb 05 19:20:12 2020 -0500 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@VERSION@">0.6.22.post1</token> - <token name="@GALAXY_VERSION@">galaxy2</token> + <token name="@GALAXY_VERSION@">galaxy3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">anndata</requirement> |
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| diff -r 080eab96d846 -r 32e547223c9e test-data/dropletutils_input.h5 |
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| Binary file test-data/dropletutils_input.h5 has changed |