diff qualimap_macros.xml @ 0:ac607906f10a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_macros.xml	Thu Oct 10 17:42:04 2019 -0400
@@ -0,0 +1,40 @@
+<macros>
+    <token name="@VERSION@">2.2.2c</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">qualimap</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btv566</citation>
+            <citation type="doi">10.1093/bioinformatics/bts503</citation>
+            <yield />
+        </citations>
+    </xml>
+
+    <token name="@SET_JAVA_OPTS@">
+        export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m"
+    </token>
+
+    <token name="@MASSAGE_OUTPUT@"><![CDATA[
+        sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' &&
+        mkdir '${output_html.extra_files_path}' &&
+        mv results/css/*.css '${output_html.extra_files_path}' &&
+        mv results/css/*.png '${output_html.extra_files_path}' &&
+        if [ -d results/images_${report_name} ]; then
+          mv results/images_${report_name}/* '${output_html.extra_files_path}' &&
+          for file in \$(ls -A results/raw_data_${report_name}); do mv "results/raw_data_${report_name}/\$file" `echo "results/\$file" | sed 's/(//;s/)//'`; done
+        fi
+        #if $summary_report:
+          && mv results/$summary_report results/summary_report.txt
+        #end if
+    ]]></token>
+</macros>