--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/salmon_plugin.xml	Mon Sep 02 14:22:54 2024 +0000
@@ -0,0 +1,62 @@
+<macros>
+    <!-- not yet finished -->
+    <token name="@SALMON_COMMAND@"><![CDATA[
+        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+            @CREATE_REPEAT_DIR_2@
+            #if str($repeat2.type.type) == "meta"
+                #for $k, $file in enumerate($repeat2.type.input)
+                    #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
+                    #set file_path = os.path.join($file_dir, 'meta_info.json')
+                    mkdir '$file_dir' &&
+                    ln -s '$file' '$file_path' &&
+                #end for
+            #elif str($repeat2.type.type) == "fld"
+                #for $k, $file in enumerate($repeat2.type.input)
+                    #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
+                    #set file_path = os.path.join($file_dir,'flenDist.txt')
+                    mkdir '$file_dir' &&
+                    ln -s '$file' '$file_path' &&
+                #end for
+            #end if
+        #end for
+    ]]></token>
+    <xml name="salmon_form">
+
+    </xml>
+    <!-- add here your test files and tests, the more stringent the better -->
+    <xml name="salmon_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="trimmomatic"/>
+                    <param name="input" value="trimmomatic.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="cutadapt_trimmed_sequences_plot"/>
+                    <has_text text="All-in-one FASTQ preprocessor"/>
+                    <has_text text="trimmomatic_plot"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="dataset_33"/>
+                    <has_text text="R1_fq"/>
+                    <has_text text="result_right"/>
+                    <has_text text="25839_merged"/>
+                    <has_text text="C2"/>
+                    <has_n_lines n="11"/>
+                    <has_n_columns n="22"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="29"/>
+        </test>
+    </xml>
+</macros>