# HG changeset patch
# User iuc
# Date 1721751900 0
# Node ID 88192fe25375378d77d64d013e8a16baa3a19d3e
# Parent  b9013e0e2b00053f4b9b9b4725c937750d705875
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 04112de6f91d4f848fe35d857c84c4b8a9fc980f

diff -r b9013e0e2b00 -r 88192fe25375 macros.xml
--- a/macros.xml	Wed Jul 17 05:54:41 2024 +0000
+++ b/macros.xml	Tue Jul 23 16:25:00 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.6.4</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
diff -r b9013e0e2b00 -r 88192fe25375 peaks_and_motif_analysis.xml
--- a/peaks_and_motif_analysis.xml	Wed Jul 17 05:54:41 2024 +0000
+++ b/peaks_and_motif_analysis.xml	Tue Jul 23 16:25:00 2024 +0000
@@ -152,9 +152,7 @@
 )
 
 #end if
-#if $method.method != 'pp.make_peak_matrix'
 @CMD_anndata_write_outputs@
-#end if
     ]]></configfile>
     </configfiles>
     <inputs>
@@ -336,13 +334,13 @@
                     <has_text_matching expression="counting_strategy = 'insertion'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" location="https://zenodo.org/records/12751925/files/pp.make_peak_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
+            <output name="anndata_out" location="https://zenodo.org/records/12800783/files/pp.make_peak_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
         </test>
         <test expect_num_outputs="3">
             <!-- tl.marker_regions -->
             <conditional name="method">
                 <param name="method" value="tl.marker_regions"/>
-                <param name="adata" location="https://zenodo.org/records/11260316/files/pp.make_peak_matrix.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/12800783/files/pp.make_peak_matrix.pbmc_500_chr21.h5ad"/>
                 <param name="groupby" value="leiden"/>
                 <param name="pvalue" value="0.1"/>
                 <param name="out_file" value="png"/>
@@ -360,14 +358,14 @@
                     <expand macro="render_plot_matching_text"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" location="https://zenodo.org/records/11260316/files/tl.marker_regions.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
-            <output name="out_png" location="https://zenodo.org/records/11260316/files/tl.marker_regions.pbmc_500_chr21.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
+            <output name="anndata_out" location="https://zenodo.org/records/12800783/files/tl.marker_regions.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
+            <output name="out_png" location="https://zenodo.org/records/12800783/files/tl.marker_regions.pbmc_500_chr21.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
         </test>
         <test expect_num_outputs="4">
             <!-- tl.diff_test single_group -->
             <conditional name="method">
                 <param name="method" value="tl.diff_test"/>
-                <param name="adata" location="https://zenodo.org/records/11260316/files/tl.marker_regions.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/12800783/files/tl.marker_regions.pbmc_500_chr21.h5ad"/>
                 <param name="merged_peaks" location="https://zenodo.org/records/11260316/files/merged_peaks.tabular"/>
                 <param name="group_key" value="leiden"/>
                 <conditional name="compare">
@@ -390,21 +388,21 @@
                     <has_text_matching expression="group2 = '2'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" location="https://zenodo.org/records/11260316/files/tl.diff_test.single_group.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
+            <output name="anndata_out" location="https://zenodo.org/records/12800783/files/tl.diff_test.single_group.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
             <output name="diff_peaks" >
                 <assert_contents>
-                    <has_text_matching expression="chr21:14215000-14220000\t-1.5951.*\t0.0016.*\t0.0563.*"/>
-                    <has_text_matching expression="chr21:17690000-17695000\t2.2792.*\t0.0996.*\t0.2127.*"/>
-                    <has_text_matching expression="chr21:13975000-13980000\t0.5423.*\t0.9829.*\t0.9829.*"/>
+                    <has_text_matching expression="chr21:17512734-17513235\t-4.0297.*\t4.3713.*\t0.0016.*"/>
+                    <has_text_matching expression="chr21:33384757-33385258\t0.278.*\t0.1502.*\t0.2644.*"/>
+                    <has_text_matching expression="chr21:42683799-42684300\t-0.438.*\t0.992.*\t0.992.*"/>
                 </assert_contents>
             </output>
-            <output name="out_png" location="https://zenodo.org/records/11260316/files/tl.diff_test.single_group.pbmc_500_chr21.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
+            <output name="out_png" location="https://zenodo.org/records/12800783/files/tl.diff_test.single_group.pbmc_500_chr21.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
         </test>
         <test expect_num_outputs="4">
             <!-- tl.diff_test background_group -->
             <conditional name="method">
                 <param name="method" value="tl.diff_test"/>
-                <param name="adata" location="https://zenodo.org/records/11260316/files/tl.marker_regions.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/12800783/files/tl.marker_regions.pbmc_500_chr21.h5ad"/>
                 <param name="merged_peaks" location="https://zenodo.org/records/11260316/files/merged_peaks.tabular"/>
                 <param name="group_key" value="leiden"/>
                 <conditional name="compare">
@@ -428,13 +426,15 @@
                     <has_text_matching expression="group1 = '1'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" location="https://zenodo.org/records/11260316/files/tl.diff_test.background_group.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
+            <output name="anndata_out" location="https://zenodo.org/records/12800783/files/tl.diff_test.background_group.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
             <output name="diff_peaks" >
                 <assert_contents>
-                    <has_text_matching expression="chr21:13880000-13885000"/>
+                    <has_text_matching expression="chr21:5123633-5124134"/>
+                    <has_text_matching expression="chr21:32403055-32403556"/>
+                    <has_text_matching expression="chr21:36156247-36156748"/>
                 </assert_contents>
             </output>
-            <output name="out_png" location="https://zenodo.org/records/11260316/files/tl.diff_test.background_group.pbmc_500_chr21.png" ftype="png" compare="sim_size" delta_frac="0.5"/>
+            <output name="out_png" location="https://zenodo.org/records/12800783/files/tl.diff_test.background_group.pbmc_500_chr21.png" ftype="png" compare="sim_size" delta_frac="0.5"/>
         </test>
     </tests>
     <help><![CDATA[