Mercurial > repos > iuc > multiqc

changeset 28:31c42a2c02d3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 7f250f4b9484eceef360ba62ef519c94b56c0b97
author iuc
date Wed, 19 Feb 2025 16:01:14 +0000
parents 7591bce96601
children
files image_content_plugin.xml macros.xml multiqc.xml porechop_plugin.xml test-data/test_image.png
diffstat 5 files changed, 23 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/image_content_plugin.xml	Wed Feb 19 16:01:14 2025 +0000
@@ -0,0 +1,14 @@
+<macros>
+    <token name="@IMAGE_CONTENT_COMMAND@"><![CDATA[
+        #for $file in $image_content_input
+            #set identifier = re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))
+            #set file_parts = str($file.element_identifier).rsplit('.', 1)
+            #set file_path = os.path.join('multiqc_WDir/', file_parts[0] + '_mqc.' + str($file.ext))
+            ln -s '$file' '$file_path' &&
+        #end for
+    ]]></token>
+    <xml name="image_content_form">
+        <param name="image_content_input" type="data" format="png,jpg,gif,tiff" multiple="true" label="Image content" help="Images to be added to the MutliQC HTML report" optional="true"/>
+    </xml>
+    <!--Test can be found in porechop_plugin.xml-->
+</macros>
--- a/macros.xml	Tue Feb 18 23:18:25 2025 +0000
+++ b/macros.xml	Wed Feb 19 16:01:14 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.27</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">multiqc</xref>
--- a/multiqc.xml	Tue Feb 18 23:18:25 2025 +0000
+++ b/multiqc.xml	Wed Feb 19 16:01:14 2025 +0000
@@ -37,6 +37,7 @@
         <import>nonpareil_plugin.xml</import>
         <import>gtdbtk_plugin.xml</import>
         <import>sambamba_plugin.xml</import>
+        <import>image_content_plugin.xml</import>
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements"/>
@@ -195,6 +196,10 @@
     #end if
 #end for
 
+#if str($image_content_input) != "None"
+    @IMAGE_CONTENT_COMMAND@
+#end if
+
 multiqc multiqc_WDir
 --filename 'report'
 
@@ -464,6 +469,7 @@
                 </when>
             </conditional>
         </repeat>
+        <expand macro="image_content_form"/>
         <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header">
             <sanitizer invalid_char="">
                 <valid initial="string.letters,string.digits">
@@ -537,7 +543,6 @@
         <expand macro="nonpareil_test"/>
         <expand macro="gtdbtk_test"/>
         <expand macro="sambamba_test"/>
-
         <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
 
     </tests>
--- a/porechop_plugin.xml	Tue Feb 18 23:18:25 2025 +0000
+++ b/porechop_plugin.xml	Wed Feb 19 16:01:14 2025 +0000
@@ -14,6 +14,7 @@
                     <param name="input" value="porechop.log"/>
                 </conditional>
             </repeat>
+            <param name="image_content_input" value="test_image.png"/>
             <param name="title" value="Title of the report"/>
             <param name="comment" value="Commment for the report"/>
             <param name="flat" value="true"/>
@@ -25,6 +26,7 @@
                     <has_text text="Porechop"/>
                     <has_text text="Reads adapter-trimmed read end"/>
                     <has_text text="Middle split reads"/>
+                    <has_text text="test image"/>
                 </assert_contents>
             </output>
             <output name="stats">
Binary file test-data/test_image.png has changed