diff rdeval_report.xml @ 4:7bf95986aaa4 draft

planemo upload for repository https://github.com/vgl-hub/rdeval commit 0d51c740073961b52774f611929f062b06de80da

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rdeval_report.xml	Wed Apr 23 19:31:12 2025 +0000
@@ -0,0 +1,40 @@
+<tool id="rdeval_report" name="rdeval report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Read summary and figures.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+    mkdir render &&
+    cd render &&
+    export RDEVAL_SHARE_DIR="\$(dirname \$(dirname \$(type -P rdeval)))/share/rdeval" &&
+    ln -s "\$RDEVAL_SHARE_DIR/figures.Rmd" &&
+    ln -s "\$RDEVAL_SHARE_DIR/rdeval_interface.R" &&
+    #set $num_files = 0
+    #for $input_file in $input_files
+        ln -s '$input_file' '${num_files}.rd' &&
+        #set $num_files += 1
+    #end for
+    R -e "rmarkdown::render('figures.Rmd', output_file='$html_outfile')" --args #for $idx in range($num_files)# '${idx}.rd' #end for
+	]]></command>
+    <inputs>
+        <param name="input_files" type="data" format="data" multiple="true" label="Input dataset" help="RD files"/>
+    </inputs>
+    <outputs>
+        <data name="html_outfile" format="html" label="Rdeval report"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_files" value="test.rd"/>
+            <output name="html_outfile" ftype="html">
+                <assert_contents>
+                    <has_size size="833000" delta="8330"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool creates a report containing a read summary and figures from input RD files.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>