--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,71 @@
+<macros>
+<token name="@FASTQC_COMMAND@"><![CDATA[
+    #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+        @CREATE_REPEAT_DIR_1@
+        #if str($repeat2.type) == "data"
+            #for $k, $file in enumerate($repeat2.input)
+                #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
+                #set file_path = os.path.join($file_dir, 'fastqc_data.txt')
+                mkdir '$file_dir' &&
+                ln -s '$file' '$file_path' &&
+            #end for
+        #elif str($repeat2.type) == "theoretical_gc"
+            #for $file in $repeat2.input
+                @ESCAPE_IDENTIFIER@
+                #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc')
+                ln -s '$file' '$file_path' &&
+            #end for
+        #end if
+    #end for
+]]></token>
+
+<xml name="fastqc_form">
+    <repeat name="output" title="FastQC output" min="1">
+        <param name="type" type="select" label="Type of FastQC output?">
+            <option value="data">Raw data</option>
+            <option value="theoretical_gc">Theorectical GC</option>
+        </param>
+        <param name="input" type="data" format="txt" multiple="true" label="FastQC output">
+            <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator>
+        </param>
+    </repeat>
+</xml>
+
+<!-- add here your test files and tests, the more stringent the better -->
+<xml name="fastqc_test">
+    <test expect_num_outputs="3">
+        <repeat name="results">
+            <conditional name="software_cond">
+                <param name="software" value="fastqc" />
+                <repeat name="output">
+                    <param name="type" value="data"/>
+                    <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
+                </repeat>
+            </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="fastqc_seq_heatmap_key_t" />
+            </assert_contents>
+        </output>
+        <output name="stats">
+            <assert_contents>
+                <has_text text="poulet5_1"/>
+                <has_text text="poulet5_2"/>
+                <has_text text="FastQC_mqc_generalstats_fastqc_median_sequence_length"/>
+                <has_n_lines n="3"/>
+                <has_n_columns n="7"/>
+            </assert_contents>
+        </output>
+        <output_collection name="plots" type="list" count="7"/>
+    </test>
+</xml>
+
+
+</macros>