--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu May 16 13:15:05 2024 +0000
@@ -0,0 +1,187 @@
+<macros>
+	<token name="@TOOL_VERSION@">2.5.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
+    <xml name="requirements">
+        <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
+        <requirement type="package" version="5.18.0">plotly</requirement>
+        <requirement type="package" version="0.2.1">python-kaleido</requirement>
+        <requirement type="package" version="0.19.19">polars</requirement>
+        <requirement type="package" version="14.0.1">pyarrow</requirement>
+        <requirement type="package" version="0.11.3">python-igraph</requirement>
+        <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>
+        <yield />
+    </xml>
+
+    <token name="@PREP_ADATA@"><![CDATA[
+        cp '$method.adata' 'anndata.h5ad' &&
+        ]]>
+    </token>
+
+    <token name="@CMD@"><![CDATA[
+        cat '$script_file' > '$hidden_output' &&
+        python '$script_file' >> '$hidden_output' &&
+		touch 'anndata_info.txt' &&
+		cat 'anndata_info.txt' @CMD_prettify_stdout@
+        ]]>
+    </token>
+
+    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'
+    ]]></token>
+
+    <token name="@CMD_imports@"><![CDATA[
+import snapatac2 as sa
+import os
+    ]]>
+    </token>
+    <xml name="sanitize_query" token_validinitial="string.printable">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <remove value="&apos;" />
+            </valid>
+        </sanitizer>
+    </xml>
+
+    <xml name="inputs_anndata">
+        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
+    </xml>
+
+    <token name="@CMD_read_inputs@"><![CDATA[
+
+adata = sa.read('anndata.h5ad', backed = None)
+]]>
+    </token>
+
+    <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"/>
+    </xml>
+
+    <xml name="param_groupby">
+        <param argument="groupby" type="text" label="The key of the observation grouping to consider">
+            <expand macro="sanitize_query" />
+        </param>
+    </xml>
+
+    <xml name="out_file">
+        <param name="out_file" type="select" optional="true" label="Type of output file">
+            <option value="png" selected="true">PNG</option>
+            <option value="svg">SVG</option>
+            <option value="pdf">PDF</option>
+		</param>
+    </xml>
+    <token name="@CMD_anndata_write_outputs@"><![CDATA[
+adata.write('anndata.h5ad')
+with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
+    print(adata, file=ainfo)
+]]>
+    </token>
+    <xml name="inputs_common_advanced">
+        <section name="advanced_common" title="Advanced Options" expanded="false">
+            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
+        </section>
+    </xml>
+    <xml name="params_render_plot">
+        <param argument="width" type="integer" value="600" label="Width of the plot"/>
+        <param argument="height" type="integer" value="400" label="Height of the plot"/>
+        <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"/>
+    </xml>
+    <xml name="param_chunk_size" tokens="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="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>
+    <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."/>
+    </xml>
+    <xml name="param_random_state">
+        <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/>
+    </xml>
+    <xml name="param_key_added" tokens="key_added">
+        <param argument="key_added" type="text" value="@KEY_ADDED@"  label="`adata.obs` key under which t add cluster labels"/>
+    </xml>
+    <xml name="param_use_rep">
+        <param argument="use_rep" type="text" value="X_spectral" label="Use the indicated representation in `.obsm`"/>
+    </xml>
+    <xml name="genome_fasta">
+        <param argument="genome_fasta" type="text" label="A fasta file containing the genome sequences or a Genome object"/>
+    </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>
+    </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"/>
+    </xml>
+    <xml name="param_network">
+        <param argument="network" type="text" label="network"/>
+    </xml>
+    <xml name="param_n_iterations">
+        <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform"
+            help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41592-023-02139-9</citation>
+        </citations>
+    </xml>
+    <xml name="render_plot_test">
+    	<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="height = 450"/>
+    </xml>
+    <xml name="param_counting_strategy">
+        <param argument="counting_strategy" type="select" label="he strategy to compute feature counts">
+            <option value="fragment">fragment</option>
+            <option value="insertion" selected="true">insertion</option>
+            <option value="paired-insertion">paired-insertion</option>
+        </param>
+    </xml>
+
+    <token name="@CMD_params_data_integration@"><![CDATA[
+use_rep = '$method.use_rep',
+#if $method.use_dims != ''
+#set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
+use_dims=$dims,
+#end if
+#if $method.groupby != ''
+#set $groupby = ([x.strip() for x in str($method.groupby).split(',')])
+groupby=$groupby,
+#end if
+#if $method.key_added != ''
+key_added = '$method.key_added',
+#end if
+    ]]>
+    </token>
+
+    <token name="@CMD_params_render_plot@"><![CDATA[
+    width = $method.width,
+    height = $method.height,
+    out_file = 'plot.$method.out_file',
+    ]]>
+    </token>
+</macros>