Mercurial > repos > iuc > snapatac2_preprocessing

diff macros.xml @ 1:cec3e76eaf05 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 15:20:02 +0000
parents 00a6721e1f81
children 48d9421bf176
line wrap: on
line diff
--- a/macros.xml	Thu May 16 13:17:14 2024 +0000
+++ b/macros.xml	Thu May 23 15:20:02 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">