--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build_matrix.xml	Tue Apr 18 13:19:11 2023 +0000
@@ -0,0 +1,108 @@
+<tool id="episcanpy_build_matrix" name="Build count matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>with EpiScanpy</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+bgzip -c '$fragment_file' > fragments.gz &&
+tabix -p bed fragments.gz &&
+cat '$script_file' > '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+touch 'anndata_info.txt' &&
+cat 'anndata_info.txt' @CMD_prettify_stdout@
+      ]]></command>
+    <configfiles>
+        <configfile name="script_file"><![CDATA[
+@CMD_imports@
+peaks = esc.ct.load_peaks('$peaks_file')
+esc.ct.norm_peaks(peaks, extension=$extension)
+esc.ct.bld_mtx_bed(
+    fragment_file='fragments.gz',
+    feature_region=peaks,
+    #if $reference_chr.chr_select == 'custom'
+        #set $chromosomes = ([x.strip() for x in str($reference_chr.chromosomes).split(',')])
+        chromosomes=$chromosomes,
+    #else
+        chromosomes='$reference_chr.chr_select',
+    #end if
+    save='anndata.h5ad')
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="fragment_file" type="data" format="bed" label="ATAC fragments file" />
+        <param name="peaks_file" type="data" format="tabular" label="Features file" help="Peaks BED file or MACS2 narrowPeak file"/>
+        <param name="extension" type="integer" value="0" min="0" label="Number of bases to extend both sides of peaks" />
+        <conditional name="reference_chr">
+            <param name="chr_select" type="select" label="Select the chromosomes of the species you are considering" >
+                <option value="human">Human chromosomes ['1', '2', '3', ... , '22', 'X', 'Y']</option>
+                <option value="mouse">Mouse chromosomes ['1', '2', '3', ... ', '19', 'X', 'Y']</option>
+                <option value="custom">Custom list of chromosomes</option>
+            </param>
+            <when value="human" />
+            <when value="mouse" />
+            <when value="custom">
+                <param name="chromosomes" value="" type="text" label="Enter comma seperated list of chromosome ids (without chr prefix)" >
+                    <expand macro="sanitize_query" />
+                </param>
+            </when>
+        </conditional>
+        <expand macro="inputs_common_advanced"/>
+    </inputs>
+    <outputs>
+        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix"/>
+        <data name="hidden_output" format="txt" label="Log file" hidden="true" >
+            <filter>advanced_common['show_log']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <!-- count matrix -->
+            <param name="fragment_file" value="chrY.fragments.bed" />
+            <param name="peaks_file" value="chrY.peaks.bed" />
+            <conditional name="reference_chr">
+                <param name="chr_select" value="custom" />
+                <param name="chromosomes" value="Y" />
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="anndata_out" file="chrY.h5ad" ftype="h5ad" compare="sim_size"/>
+        </test>
+    </tests>
+  <help>
+.. class:: infomark
+
+**What it does**
+
+Builds single-cell ATAC-seq count matrix in Anndata format.  
+
+-----
+
+**Inputs**
+
+- ATAC fragments containing the positions of Tn5 integration sites, the cell barcode that the DNA fragment originated from, and the number of times the fragment was sequenced. An example::
+
+    chrY	2650256	2650533	GACCAATGTCCGTAGC	1
+    chrY	2650420	2650463	TGACAACGTACTTCAG	1
+    chrY	2650444	2650643	GTGGATTGTACAAGCG	3
+    chrY	2650639	2650990	ATAGGCTAGGGCTCTC	2
+    chrY	2650650	2650692	GACTAACAGCAACGGT	1
+    chrY	2650699	2650942	TCAAAGCTCAAAGTAG	1
+    chrY	2650768	2650809	TTGTTGTAGGGCATTG	2
+    chrY	2650841	2650873	TTGTTGTAGGGCATTG	1
+    chrY	2650957	2650995	GACTAACAGCAACGGT	1
+    chrY	2651205	2651265	TCAAAGCTCAAAGTAG	1
+    chrY	2651215	2651268	TCACAAGGTCAAGACG	1
+
+- Features file. A plain BED file with peak locations or narrowPeak file from MACS2.
+
+**Output**
+
+- Count matrix in Anndata format.
+
+  </help>
+    <expand macro="citations"/>
+</tool>