Mercurial > repos > iuc > anndata_import

changeset 5:32e547223c9e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
author iuc
date Wed, 05 Feb 2020 19:20:12 -0500
parents 080eab96d846
children 00712416fdaa
files import.xml macros.xml test-data/dropletutils_input.h5
diffstat 3 files changed, 26 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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**
--- a/macros.xml	Sat Jan 18 03:36:57 2020 -0500
+++ b/macros.xml	Wed Feb 05 19:20:12 2020 -0500
@@ -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>
Binary file test-data/dropletutils_input.h5 has changed