--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,62 @@
+<macros>
+    <token name="@QUALIMAP_COMMAND@"><![CDATA[
+        #for $file in $repeat.software_cond.input
+            #if re.search("genome_results", str($file.element_identifier))
+                sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" &&
+                dir_name="$software_dir/\${sample}" &&
+                mkdir -p \${dir_name} &&
+                filepath_1="\${dir_name}/genome_results.txt" &&
+                ln -sf '$file' \${filepath_1} &&
+            #elif re.search("coverage_histogram", str($file.element_identifier))
+                nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
+                mkdir -p \${nested_dir_name} &&
+                filepath_2="\${nested_dir_name}/coverage_histogram.txt" &&
+                ln -sf '$file' \${filepath_2} &&
+            #elif re.search("gc-content_distribution", str($file.element_identifier))
+                nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
+                mkdir -p \${nested_dir_name} &&
+                filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" &&
+                ln -sf '$file' \${filepath_3} &&
+            #else
+                #pass
+            #end if
+        #end for
+    ]]></token>
+    <xml name="qualimap_form">
+        <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report"/>
+    </xml>
+    <!-- add here your test files and tests, the more stringent the better -->
+    <xml name="qualimap_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="qualimap"/>
+                    <param name="input" value="genome_results.txt"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="qualimap"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_mean_coverage"/>
+                    <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_mapped_reads"/>
+                    <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_total_reads"/>
+                    <has_text text="x_bam"/>
+                    <has_text text="0.98"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="6"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+    </xml>
+</macros>