# HG changeset patch
# User iuc
# Date 1670671338 0
# Node ID abfd8a6544d7db414e7953353b55f8c60ff1325c
# Parent  9a913cdee30ebeae7dec35170e9233668cc4ccea
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a

diff -r 9a913cdee30e -r abfd8a6544d7 macros.xml
--- a/macros.xml	Wed Nov 03 15:17:39 2021 +0000
+++ b/macros.xml	Sat Dec 10 11:22:18 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.11</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">multiqc</xref>
@@ -218,9 +218,11 @@
                     #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls')
                     ln -s '$file' '$file_path' &&
                 #end for
-            #elif str($repeat2.type.type) == "junction_annotation"
-                #set $pattern = "Group               Total_bases         Tag_count           Tags/Kb"
-                @LN_3_FILES@
+            #elif str($repeat2.type.type) == "junction_saturation"
+                #for $k, $file in enumerate($repeat2.type.input)
+                #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.junctionSaturation_plot.r')
+                    ln -s '${file}' '$file_path' &&
+                #end for
             #elif str($repeat2.type.type) == "read_distribution"
                 #set $pattern = "Group               Total_bases         Tag_count           Tags/Kb"
                 @LN_3_FILES@
diff -r 9a913cdee30e -r abfd8a6544d7 multiqc.xml
--- a/multiqc.xml	Wed Nov 03 15:17:39 2021 +0000
+++ b/multiqc.xml	Sat Dec 10 11:22:18 2022 +0000
@@ -413,42 +413,42 @@
                     <repeat name="output" title="RSeQC output" min="1">
                         <conditional name="type">
                             <param name="type" type="select" label="Type of RSeQC output?">
-                                <option value="bam_stat">bam_stat</option>
-                                <option value="gene_body_coverage">gene_body_coverage</option>
-                                <option value="infer_experiment">infer_experiment</option>
-                                <option value="inner_distance">inner_distance</option>
-                                <option value="junction_annotation">junction_annotation</option>
-                                <option value="junction_saturation">junction_saturation</option>
-                                <option value="read_distribution">read_distribution</option>
-                                <option value="read_duplication_pos">read_duplication_pos</option>
-                                <option value="read_gc">read_gc</option>
+                                <option value="bam_stat">BAM/SAM mapping stats</option>
+                                <option value="gene_body_coverage">Gene body coverage</option>
+                                <option value="infer_experiment">Infer experiment</option>
+                                <option value="inner_distance">Inner distance</option>
+                                <option value="junction_annotation">Junction annotation</option>
+                                <option value="junction_saturation">Junction saturation</option>
+                                <option value="read_distribution">Read distribution</option>
+                                <option value="read_duplication_pos">Read duplication</option>
+                                <option value="read_gc">Read GC</option>
                             </param>
                             <when value="bam_stat">
-                                <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC bam_stat output" help="It should contain 'Proper-paired reads map to different chrom:'"/>
+                                <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC BAM stat: output file" help="It should contain 'Proper-paired reads map to different chrom:'"/>
                             </when>
                             <when value="gene_body_coverage">
-                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene_body_coverage output"/>
+                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene body coverage:  stats file"/>
                             </when>
                             <when value="infer_experiment">
-                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer_experiment output" help="It should contain 'Fraction of reads explained by'"/>
+                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer experiment: configuration output" help="It should contain 'Fraction of reads explained by'"/>
                             </when>
                             <when value="inner_distance">
-                                <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC inner_distance output"/>
+                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC inner distance: frequency file"/>
                             </when>
                             <when value="junction_annotation">
-                                <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC junction_annotation output" help="It should contain 'Partial Novel Splicing Junctions:'"/>
+                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction annotation: stats file" help="It should contain 'Partial Novel Splicing Junctions:'"/>
                             </when>
                             <when value="junction_saturation">
-                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction_saturation output"/>
+                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction saturation: junction saturation plot Rscript file"/>
                             </when>
                             <when value="read_distribution">
-                                <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC read_distribution output" help="It should contain 'Group               Total_bases         Tag_count           Tags/Kb'"/>
+                                <param name="input" type="data" format="txt" multiple="true" label="RSeQC read distribution: stats output" help="It should contain 'Group               Total_bases         Tag_count           Tags/Kb'"/>
                             </when>
                             <when value="read_duplication_pos">
-                                <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_duplication_pos output"/>
+                                <param name="input" type="data" format="xls" multiple="true" label="RSeQC read duplication: positions XLS file"/>
                             </when>
                             <when value="read_gc">
-                                <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_gc output"/>
+                                <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read GC output"/>
                             </when>
                         </conditional>
                     </repeat>
@@ -1076,6 +1076,36 @@
             </output>
 	    <output_collection name="stats" type="list" count="2"/>
         </test>
+        <!--Test 07-->
+        <test expect_num_outputs="2">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="rseqc" />
+                    <repeat name="output">
+                        <conditional name="type">
+                            <param name="type" value="junction_annotation"/>
+                            <param name="input" value="junction_annotation.txt"/>
+                        </conditional>
+                    </repeat>
+                    <repeat name="output">
+                        <conditional name="type">
+                            <param name="type" value="junction_saturation"/>
+                            <param name="input" value="junction_saturation.txt"/>
+                        </conditional>
+                    </repeat>
+                </conditional>
+            </repeat>
+            <param name="title" value="RSEQC report"/>
+            <!-- <param name="flat" value="true"/> -->
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="RSEQC report" />
+                    <has_text text="Junction Annotation" />
+                    <has_text text="Junction Saturation" />
+                </assert_contents>
+            </output>
+	        <output_collection name="stats" type="list" count="2"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r 9a913cdee30e -r abfd8a6544d7 test-data/junction_annotation.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/junction_annotation.txt	Sat Dec 10 11:22:18 2022 +0000
@@ -0,0 +1,18 @@
+Reading reference bed file:  /tmp/tmpwdbqfb2i/files/000/dataset_3.dat  ...  Done
+Load BAM file ...  Done
+
+===================================================================
+Total splicing  Events:	4
+Known Splicing Events:	1
+Partial Novel Splicing Events:	1
+Novel Splicing Events:	1
+Filtered Splicing Events:	1
+
+Total splicing  Junctions:	3
+Known Splicing Junctions:	1
+Partial Novel Splicing Junctions:	1
+Novel Splicing Junctions:	1
+
+===================================================================
+Create BED file ...
+Create Interact file ...
diff -r 9a913cdee30e -r abfd8a6544d7 test-data/junction_saturation.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/junction_saturation.txt	Sat Dec 10 11:22:18 2022 +0000
@@ -0,0 +1,12 @@
+pdf('output.junctionSaturation_plot.pdf')
+x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)
+y=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1)
+z=c(0,0,0,0,0,0,1,1,1,1,1,1,1,2,2,2,2,2,2,3)
+w=c(0,0,0,0,0,0,1,1,1,1,1,1,1,2,2,2,2,2,2,2)
+m=max(0,0,0)
+n=min(0,0,0)
+plot(x,z/1000,xlab='percent of total reads',ylab='Number of splicing junctions (x1000)',type='o',col='blue',ylim=c(n,m))
+points(x,y/1000,type='o',col='red')
+points(x,w/1000,type='o',col='green')
+legend(5,0, legend=c("All junctions","known junctions", "novel junctions"),col=c("blue","red","green"),lwd=1,pch=1)
+dev.off()