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changeset 26:d2aaac19f42f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
author iuc
date Tue, 11 Feb 2025 10:13:08 +0000
parents a7e081ceb76a
children
files macros.xml multiqc.xml sambamba_plugin.xml test-data/sambamba.txt
diffstat 4 files changed, 61 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Sat Jan 25 17:24:12 2025 +0000
+++ b/macros.xml	Tue Feb 11 10:13:08 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.27</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">multiqc</xref>
--- a/multiqc.xml	Sat Jan 25 17:24:12 2025 +0000
+++ b/multiqc.xml	Tue Feb 11 10:13:08 2025 +0000
@@ -23,6 +23,7 @@
         <import>star_plugin.xml</import>
         <import>trimmomatic_plugin.xml</import>
         <import>vcftools_plugin.xml</import>
+        <import>sambamba_plugin.xml</import>
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements"/>
@@ -143,6 +144,8 @@
         @TRIMMOMATIC_COMMAND@
     #elif str($repeat.software_cond.software) == "vcftools"
         @VCFTOOLS_COMMAND@
+    #elif str($repeat.software_cond.software) == "sambamba"
+        @SAMBAMBA_COMMAND@
     #else if str($repeat.software_cond.software) == "custom_content":
         #set $configfile = "T"
         #for $j, $file in enumerate( $repeat.software_cond.input )
@@ -236,6 +239,7 @@
                     <!--<option value="salmon">Salmon</option>-->
                     <option value="samblaster">Samblaster</option>
                     <option value="samtools">Samtools</option>
+                    <option value="sambamba">Sambamba</option>
                     <!--<option value="sargasso">Sargasso</option>-->
                     <!--<option value="seqyclean">SeqyClean</option>-->
                     <!--<option value="sexdeterrmine">SexDetErrmine</option>-->
@@ -349,6 +353,9 @@
                 <when value="vcftools">
                     <expand macro="vcftools_form"/>
                 </when>
+                <when value="sambamba">
+                    <expand macro="sambamba_form"/>
+                </when>
                 <when value="custom_content">
                     <param argument="plot_type" label="The plot type to visualise the data with" type="select">
                         <option value="linegraph">linegraph</option>
@@ -425,6 +432,7 @@
         <expand macro="gatk_test"/>
         <expand macro="bamtools_test"/>
         <expand macro="pycoqc_test"/>
+        <expand macro="sambamba_test"/>
 
         <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sambamba_plugin.xml	Tue Feb 11 10:13:08 2025 +0000
@@ -0,0 +1,39 @@
+<macros>
+    <token name="@SAMBAMBA_COMMAND@"><![CDATA[
+        #set $pattern = "finding positions of the duplicate reads in the file"
+        @LN_FILES@
+    ]]></token>
+    <xml name="sambamba_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Output of Sambamba markdup" help="It should contain 'finding positions of the duplicate reads in the file'"/>
+    </xml>
+    <xml name="sambamba_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="sambamba"/>
+                    <param name="input" value="sambamba.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="Sambamba Markdup"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="Sample"/>
+                    <has_text text="sambamba_markdup-duplicate_rate"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sambamba.txt	Tue Feb 11 10:13:08 2025 +0000
@@ -0,0 +1,13 @@
+
+sambamba 1.0.1
+ by Artem Tarasov and Pjotr Prins (C) 2012-2023
+    LDC 1.39.0 / DMD v2.109.1 / LLVM17.0.6 / bootstrap LDC - the LLVM D compiler (1.39.0)
+
+finding positions of the duplicate reads in the file...
+  sorted 0 end pairs
+     and 4 single ends (among them 0 unmatched pairs)
+  collecting indices of duplicate reads...   done in 0 ms
+  found 3 duplicates
+collected list of positions in 0 min 0 sec
+marking duplicates...
+collected list of positions in 0 min 0 sec