--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cooc_mutbamscan.xml	Thu Aug 11 13:50:37 2022 +0000
@@ -0,0 +1,155 @@
+<tool id="cooc_mutbamscan" name="Cojac: mutbamscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="@PROFILE@">
+    <description>
+        scan an alignment file for mutation co-occurrences
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+ln -s '$bed_file' 'bed_file' &&
+@VOCDIR_COMMAND@
+#import re
+#set identifier = re.sub('[^\s\w\-\\.]', '_', str($bam_file.element_identifier))
+ln -s '$bam_file' ${identifier}.bam &&
+ln -s '${bam_file.metadata.bam_index}' ${identifier}.bai &&
+cooc-mutbamscan
+    -a '${identifier}.bam'
+    -b 'bed_file'
+    -m '$vocdir'
+    -y cooc.yaml
+    -j cooc.json
+    #if $amplicons_file.choice == 'build'
+        -A amplicons.yaml
+    #else
+        -Q '$amplicons_file.in_amp'
+    #end if
+    -t cooc.tsv
+    --cooc $cooc
+    ]]></command>
+    <inputs>
+        <expand macro="vocdir_input"/>
+        <param name="bed_file" type="data" format="bed"
+               label="BED file defining the amplicons"/>
+        <param name="bam_file" type="data" format="bam,cram,sam"
+               label="Alignment BAM/CRAM/SAM file"/>
+        <param argument="--cooc" type="integer" min="1" value="2"
+               label="Minimum number of cooccurence mutations on the same amplicon"/>
+        <conditional name="amplicons_file">
+            <param name="choice" type="select" label="Source of amplicons YAML file">
+                <option value="build">Build from BED + set of YAMLs for variants of concern</option>
+                <option value="custom">From history</option>
+            </param>
+            <when value="build"/>
+            <when value="custom">
+                <param name="in_amp" type="data" format="yaml"
+                       label="YAML file to query amplicons"/>
+            </when>
+        </conditional>
+        <param name="output_files" type="select" display="checkboxes"
+               multiple="true" label="Output files">
+            <option value="yaml" selected="true">YAML</option>
+            <option value="json">JSON</option>
+            <option value="tabular">tabular</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="cooc_yaml" format="yaml"
+              label="${tool.name} on ${on_string}: Mutation cooccurrence (yaml)"
+              from_work_dir="cooc.yaml">
+            <filter>'yaml' in output_files</filter>
+        </data>
+        <data name="cooc_json" format="json"
+              label="${tool.name} on ${on_string}: Mutation cooccurrence (json)"
+              from_work_dir="cooc.json">
+            <filter>'json' in output_files</filter>
+        </data>
+        <data name="cooc_tsv" format="tabular"
+              label="${tool.name} on ${on_string}: Mutation cooccurrence (tabular)"
+              from_work_dir="cooc.tsv">
+            <filter>'tabular' in output_files</filter>
+        </data>
+        <data name="amplicons" format="yaml"
+              label="${tool.name} on ${on_string}: Amplicons (yaml)"
+              from_work_dir="amplicons.yaml">
+            <filter>amplicons_file['choice'] == 'build'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- Test 1: build yaml for amplicons from bed and voc/ -->
+        <test expect_num_outputs="4">
+            <conditional name="vocdir_option">
+                <param name="choice" value="custom"/>
+                <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
+            </conditional>
+            <param name="bam_file" value="tbam11.bam"/>
+            <param name="bed_file" value="nCoV-2019.insert.V3.bed"/>
+            <conditional name="amplicons_file">
+                <param name="choice" value="build"/>
+            </conditional>
+            <param name="output_files" value="yaml,json,tabular"/>
+            <output name="cooc_yaml" ftype="yaml">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+            <output name="cooc_json" ftype="json">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+            <output name="cooc_tsv" ftype="tabular">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+            <output name="amplicons" ftype="yaml">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 2: supply yaml for amplicons and voc/ from cache -->
+        <test expect_num_outputs="2">
+            <conditional name="vocdir_option">
+                <param name="choice" value="cache"/>
+            </conditional>
+            <param name="bam_file" value="tbam11.bam"/>
+            <param name="bed_file" value="nCoV-2019.insert.V3.bed"/>
+            <conditional name="amplicons_file">
+                <param name="choice" value="custom"/>
+                <param name="in_amp" value="amplicons111.yaml"/>
+            </conditional>
+            <param name="output_files" value="yaml,tabular"/>
+            <output name="cooc_yaml" ftype="yaml">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+            <output name="cooc_tsv" ftype="tabular">
+                <assert_contents>
+                    <has_text text="76_om1"/>
+                    <has_text text="81_om1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Information about **cooc-mutbamscan** method
+============================================
+
+The method scans an alignment BAM/CRAM/SAM file for mutation co-occurrences and output a JSON or YAML file.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>