Mercurial > repos > iuc > snapatac2_plotting

changeset 1:fecf9664c885 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
author iuc
date Thu, 23 May 2024 15:19:43 +0000
parents 0cfd2d2f7351
children c01f0a08ab43
files macros.xml plotting.xml
diffstat 2 files changed, 61 insertions(+), 54 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu May 16 13:15:05 2024 +0000
+++ b/macros.xml	Thu May 23 15:19:43 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
-	<token name="@TOOL_VERSION@">2.5.3</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">2.5.3</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
@@ -12,6 +12,9 @@
         <requirement type="package" version="0.8.33">hdbscan</requirement>
         <requirement type="package" version="0.0.9">harmonypy</requirement>
         <requirement type="package" version="1.7.4">scanorama</requirement>
+        <requirement type="package" version="3.0.1">macs3</requirement>
+        <requirement type="package" version="0.70.16">multiprocess</requirement>
+        <requirement type="package" version="0.10.2">leidenalg</requirement>
         <yield />
     </xml>
 
@@ -23,8 +26,8 @@
     <token name="@CMD@"><![CDATA[
         cat '$script_file' > '$hidden_output' &&
         python '$script_file' >> '$hidden_output' &&
-		touch 'anndata_info.txt' &&
-		cat 'anndata_info.txt' @CMD_prettify_stdout@
+        touch 'anndata_info.txt' &&
+        cat 'anndata_info.txt' @CMD_prettify_stdout@
         ]]>
     </token>
 
@@ -56,7 +59,7 @@
 
     <xml name="dimentions_plot">
         <param argument="width" type="integer" value="500" label="Width of the plot"/>
-		<param argument="height" type="integer" value="400" label="Height of the plot"/>
+        <param argument="height" type="integer" value="400" label="Height of the plot"/>
     </xml>
 
     <xml name="param_groupby">
@@ -66,11 +69,11 @@
     </xml>
 
     <xml name="out_file">
-        <param name="out_file" type="select" optional="true" label="Type of output file">
+        <param name="out_file" type="select" optional="true" label="Type of output plot">
             <option value="png" selected="true">PNG</option>
             <option value="svg">SVG</option>
             <option value="pdf">PDF</option>
-		</param>
+        </param>
     </xml>
     <token name="@CMD_anndata_write_outputs@"><![CDATA[
 adata.write('anndata.h5ad')
@@ -89,28 +92,28 @@
         <expand macro="out_file"/>
     </xml>
     <xml name="param_shift">
-    	<param argument="shift_left" type="integer" value="4" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/>
-    	<param argument="shift_right" type="integer" value="-5" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/>
+        <param argument="shift_left" type="integer" value="4" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/>
+        <param argument="shift_right" type="integer" value="-5" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/>
     </xml>
     <xml name="param_chunk_size" tokens="size">
-    	<param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/>
+        <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/>
+    </xml>
+    <xml name="min_max_frag_size">
+        <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/>
+        <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/>
     </xml>
-	<xml name="min_max_frag_size">
-		<param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/>
-		<param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/>
-	</xml>
-	<xml name="params_data_integration">
-		<param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
-		<param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation">
-			<expand macro="sanitize_query"/>
-		</param>
-		<param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider">
+    <xml name="params_data_integration">
+        <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
+        <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation">
+            <expand macro="sanitize_query"/>
+        </param>
+        <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider">
             <expand macro="sanitize_query" />
         </param>
-		<param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/>
-	</xml>
+        <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/>
+    </xml>
     <xml name="param_n_comps">
-s        <param argument="n_comps" type="integer" value="30" label="Number of dimensions to keep" help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."/>
+        <param argument="n_comps" type="integer" value="30" label="Number of dimensions to keep" help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."/>
     </xml>
     <xml name="param_random_state">
         <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/>
@@ -126,12 +129,12 @@
     </xml>
     <xml name="background">
         <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background">
-			<expand macro="sanitize_query"/>
-		</param>
+            <expand macro="sanitize_query"/>
+        </param>
     </xml>
     <xml name="mat">
         <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/>
-		<param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/>
+        <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/>
     </xml>
     <xml name="param_network">
         <param argument="network" type="text" label="network"/>
@@ -147,11 +150,11 @@
         </citations>
     </xml>
     <xml name="render_plot_test">
-    	<param name="width" value="650"/>
+        <param name="width" value="650"/>
         <param name="height" value="450"/>
     </xml>
     <xml name="render_plot_matching_text">
-    	<has_text_matching expression="width = 650"/>
+        <has_text_matching expression="width = 650"/>
         <has_text_matching expression="height = 450"/>
     </xml>
     <xml name="param_counting_strategy">
--- a/plotting.xml	Thu May 16 13:15:05 2024 +0000
+++ b/plotting.xml	Thu May 23 15:19:43 2024 +0000
@@ -8,20 +8,20 @@
     <command detect_errors="exit_code"><![CDATA[
 @PREP_ADATA@
 @CMD@
-	]]></command>
+    ]]></command>
     <configfiles>
         <configfile name="script_file"><![CDATA[
 @CMD_imports@
 @CMD_read_inputs@
 
 #if $method.method == 'pl.frag_size_distr'
-	#if $method.log_scale
+    #if $method.log_scale
 fig = sa.pl.frag_size_distr(adata, show=False)
 fig.update_yaxes(type="log")
 sa.pl.render_plot(fig, @CMD_params_render_plot@)
-	#else
+    #else
 sa.pl.frag_size_distr(adata, @CMD_params_render_plot@)
-	#end if
+    #end if
 #else if $method.method == 'pl.tsse'
 sa.pl.tsse(
     adata,
@@ -30,28 +30,32 @@
 )
 #else if $method.method == 'pl.umap'
 sa.pl.umap(
-	adata,
-	color = '$method.color',
-	use_rep = '$method.use_rep',
-	marker_size = $method.marker_size,
-	marker_opacity = $method.marker_opacity,
-	sample_size = $method.sample_size,
-	@CMD_params_render_plot@
+    adata,
+    color = '$method.color',
+    use_rep = '$method.use_rep',
+    #if $method.marker_size
+    marker_size = $method.marker_size,
+    #end if
+    marker_opacity = $method.marker_opacity,
+    #if $method.sample_size
+    sample_size = $method.sample_size,
+    #end if
+    @CMD_params_render_plot@
 )
 #else if $method.method == 'pl.regions'
 sa.pl.regions(
-	adata,
-	groupby = '$method.groupby',
-	peaks = '$method.peaks',
-	@CMD_params_render_plot@
+    adata,
+    groupby = '$method.groupby',
+    peaks = '$method.peaks',
+    @CMD_params_render_plot@
 )
 #else if $method.method == 'pl.spectral_eigenvalues'
 sa.pl.spectral_eigenvalues(
-	adata,
-	@CMD_params_render_plot@
+    adata,
+    @CMD_params_render_plot@
 )
 #end if
-	]]></configfile>
+    ]]></configfile>
     </configfiles>
     <inputs>
         <conditional name="method">
@@ -106,7 +110,7 @@
             <!-- pl.frag_size_distr -->
             <conditional name="method">
                 <param name="method" value="pl.frag_size_distr"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/pp.import_data.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
                 <param name="log_scale" value="True"/>
                 <param name="out_file" value="pdf"/>
                 <expand macro="render_plot_test"/>
@@ -114,7 +118,7 @@
             <section name="advanced_common">
                 <param name="show_log" value="true"/>
             </section>
-            <output name="out_pdf" location="https://zenodo.org/records/11199963/files/pl.frag_size_distr.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
+            <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.frag_size_distr.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
             <output name="hidden_output">
                 <assert_contents>
                     <has_text_matching expression="sa.pl.frag_size_distr"/>
@@ -127,7 +131,7 @@
             <!-- pl.tsse -->
             <conditional name="method">
                 <param name="method" value="pl.tsse"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
                 <param name="min_fragment" value="500"/>
                 <param name="out_file" value="png"/>
                 <expand macro="render_plot_test"/>
@@ -142,13 +146,13 @@
                     <expand macro="render_plot_matching_text"/>
                 </assert_contents>
             </output>
-            <output name="out_png" location="https://zenodo.org/records/11199963/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
+            <output name="out_png" location="https://zenodo.org/records/11260316/files/pl.tsse.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
         </test>
         <test expect_num_outputs="2">
             <!-- pl.umap -->
             <conditional name="method">
                 <param name="method" value="pl.umap"/>
-                <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11199963/files/tl.leiden.pbmc_500_chr21.h5ad"/>
+                <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
                 <param name="color" value="leiden"/>
                 <param name="use_rep" value="X_umap"/>
                 <param name="marker_size" value="1"/>
@@ -171,13 +175,13 @@
                     <expand macro="render_plot_matching_text"/>
                 </assert_contents>
             </output>
-            <output name="out_svg" location="https://zenodo.org/records/11199963/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/>
+            <output name="out_svg" location="https://zenodo.org/records/11260316/files/pl.umap.svg" ftype="svg" compare="sim_size" delta_frac="0.1"/>
         </test>
         <test expect_num_outputs="2">
             <!-- pl.spectral_eigenvalues -->
             <conditional name="method">
                 <param name="method" value="pl.spectral_eigenvalues"/>
-                <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
+                <param name="adata" ftype="h5ad" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
                 <expand macro="render_plot_test"/>
                 <param name="out_file" value="pdf"/>
             </conditional>
@@ -190,7 +194,7 @@
                     <expand macro="render_plot_matching_text"/>
                 </assert_contents>
             </output>
-            <output name="out_pdf" location="https://zenodo.org/records/11199963/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
+            <output name="out_pdf" location="https://zenodo.org/records/11260316/files/pl.spectral_eigenvalues.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
         </test>
     </tests>
     <help><![CDATA[