# HG changeset patch
# User iuc
# Date 1547979630 18000
# Node ID 161f4383df15a9bc495708535a6abe793b680a7e
# Parent  1c2db0054039527f042f9fff271256d888a66d7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b

diff -r 1c2db0054039 -r 161f4383df15 multiqc.xml
--- a/multiqc.xml	Wed Aug 08 08:49:39 2018 -0400
+++ b/multiqc.xml	Sun Jan 20 05:20:30 2019 -0500
@@ -1,7 +1,7 @@
 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
-        <token name="@WRAPPER_VERSION@">1.6</token>
+        <token name="@WRAPPER_VERSION@">1.7</token>
         <token name="@ESCAPE_IDENTIFIER@">
 <![CDATA[
 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
@@ -372,6 +372,9 @@
                 @LN_3_FILES@
             #end if
         #end for
+    #elif str($repeat.software_cond.software) == "slamdunk"
+        #set $pattern = "# slamdunk"
+        @LN_FILES@
     #elif str($repeat.software_cond.software) == "snpeff"
         #set $pattern = "SnpEff_version"
         @LN_FILES@
@@ -539,7 +542,7 @@
                     <option value="samtools">Samtools</option>
                     <!--<option value="sargasso">Sargasso</option>-->
                     <!--<option value="skewer">Skewer</option>-->
-                    <!--<option value="slamdunk">Slamdunk</option>-->
+                    <option value="slamdunk">Slamdunk</option>
                     <option value="snpeff">SnpEff</option>
                     <option value="sortmerna">SortMeRNA</option>
                     <option value="star">STAR</option>
@@ -732,12 +735,15 @@
                         </conditional>
                     </repeat>
                 </when>
-                <when value="sortmerna">
-                    <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/>
+                <when value="slamdunk">
+                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/>
                 </when>
                 <when value="snpeff">
                     <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
                 </when>
+                <when value="sortmerna">
+                    <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/>
+                </when>
                 <when value="star">
                     <repeat name="output" title="STAR output" min="1">
                         <conditional name="type">
@@ -846,6 +852,12 @@
             </repeat>
             <repeat name="results">
                 <conditional name="software_cond">
+                    <param name="software" value="slamdunk" />
+                    <param name="input" value="slamdunk_summary.txt,slamdunk_reads1_overallrates.csv,slamdunk_reads2_overallrates.csv" />
+                </conditional>
+            </repeat>
+            <repeat name="results">
+                <conditional name="software_cond">
                     <param name="software" value="sortmerna" />
                     <param name="input" value="sortmerna.txt" />
                 </conditional>
@@ -867,6 +879,7 @@
                     <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
                     <has_text text="fastqc_seq_heatmap_key_t" />
                     <has_text text="flexbar_plot" />
+                    <has_text text="a tool to analyze SLAMSeq data" />
                     <has_text text="sortmerna-detailed-plot" />
                     <has_text text="trimmomatic_plot" />
                 </assert_contents>
@@ -878,6 +891,7 @@
                 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
                 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
+                <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/>
                 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
                 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>
             </output_collection>
diff -r 1c2db0054039 -r 161f4383df15 test-data/pre_alignment_soft_stats.tabular
--- a/test-data/pre_alignment_soft_stats.tabular	Wed Aug 08 08:49:39 2018 -0400
+++ b/test-data/pre_alignment_soft_stats.tabular	Sun Jan 20 05:20:30 2019 -0500
@@ -1,9 +1,11 @@
-Sample	SortMeRNA_mqc-generalstats-sortmerna-rRNA_pct	Trimmomatic_mqc-generalstats-trimmomatic-dropped_pct	fastp_mqc-generalstats-fastp-pct_duplication	fastp_mqc-generalstats-fastp-after_filtering_q30_rate	fastp_mqc-generalstats-fastp-after_filtering_q30_bases	fastp_mqc-generalstats-fastp-after_filtering_gc_content	fastp_mqc-generalstats-fastp-pct_surviving	fastp_mqc-generalstats-fastp-pct_adapter	Cutadapt_mqc-generalstats-cutadapt-percent_trimmed	FastQC_mqc-generalstats-fastqc-percent_duplicates	FastQC_mqc-generalstats-fastqc-percent_gc	FastQC_mqc-generalstats-fastqc-avg_sequence_length	FastQC_mqc-generalstats-fastqc-percent_fails	FastQC_mqc-generalstats-fastqc-total_sequences	Flexbar_mqc-generalstats-flexbar-removed_bases_pct
-25839_merged	1.099299750020029														
-C2		17.98													
-R1_fq			0.0	0.79021	226.0	0.367133	100.0								
-bwa-mem-fastq1_fq			0.0	0.907789	41653.0	0.479928	97.97979797979798	33.33333333333333							
-dataset_33									10.776820436239396						
-poulet5_1										36.30591159931017	48.0	101.0	8.333333333333332	267849.0	
-poulet5_2										36.173388748054116	48.0	101.0	8.333333333333332	267849.0	
-result_right															45.26066350710901
+Sample	SortMeRNA_mqc-generalstats-sortmerna-rRNA_pct	Trimmomatic_mqc-generalstats-trimmomatic-dropped_pct	fastp_mqc-generalstats-fastp-pct_duplication	fastp_mqc-generalstats-fastp-after_filtering_q30_rate	fastp_mqc-generalstats-fastp-after_filtering_q30_bases	fastp_mqc-generalstats-fastp-after_filtering_gc_content	fastp_mqc-generalstats-fastp-pct_surviving	fastp_mqc-generalstats-fastp-pct_adapter	Cutadapt_mqc-generalstats-cutadapt-percent_trimmed	FastQC_mqc-generalstats-fastqc-percent_duplicates	FastQC_mqc-generalstats-fastqc-percent_gc	FastQC_mqc-generalstats-fastqc-avg_sequence_length	FastQC_mqc-generalstats-fastqc-percent_fails	FastQC_mqc-generalstats-fastqc-total_sequences	Slamdunk_mqc-generalstats-slamdunk-counted	Slamdunk_mqc-generalstats-slamdunk-retained	Slamdunk_mqc-generalstats-slamdunk-mapped	Slamdunk_mqc-generalstats-slamdunk-sequenced	Flexbar_mqc-generalstats-flexbar-removed_bases_pct
+25839_merged	1.099299750020029																		
+C2		17.98																	
+R1_fq			0.0	0.79021	226.0	0.367133	100.0												
+bwa-mem-fastq1_fq			0.0	0.907789	41653.0	0.479928	97.97979797979798	33.33333333333333											
+dataset_33									10.776820436239396										
+poulet5_1										36.30591159931017	48.0	101.0	8.333333333333332	267849.0					
+poulet5_2										36.173388748054116	48.0	101.0	8.333333333333332	267849.0					
+reads1															16	12	12	12	
+reads2															12	6	6	6	
+result_right																			45.26066350710901
diff -r 1c2db0054039 -r 161f4383df15 test-data/slamdunk_readrates_plus.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/slamdunk_readrates_plus.tabular	Sun Jan 20 05:20:30 2019 -0500
@@ -0,0 +1,3 @@
+Sample	A>C	A>G	A>T	C>A	C>G	C>T	G>A	G>C	G>T	T>A	T>C	T>G
+slamdunk_reads1_overallrates_csv	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	3.7735849056603774	0.0
+slamdunk_reads2_overallrates_csv	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	3.260869565217391	0.0
diff -r 1c2db0054039 -r 161f4383df15 test-data/slamdunk_reads1_overallrates.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/slamdunk_reads1_overallrates.csv	Sun Jan 20 05:20:30 2019 -0500
@@ -0,0 +1,7 @@
+# slamdunk rates v0.3.3
+	A	a	C	c	G	g	T	t	N	n	
+A	93	20	0	0	0	1	0	0	0	0	
+C	0	0	106	12	0	0	0	0	0	0	
+G	0	0	0	0	82	33	0	0	0	0	
+T	0	0	4	1	0	0	102	47	0	0	
+N	0	0	0	0	0	0	0	0	0	0	
diff -r 1c2db0054039 -r 161f4383df15 test-data/slamdunk_reads2_overallrates.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/slamdunk_reads2_overallrates.csv	Sun Jan 20 05:20:30 2019 -0500
@@ -0,0 +1,7 @@
+# slamdunk rates v0.3.3
+	A	a	C	c	G	g	T	t	N	n	
+A	42	0	0	0	0	0	0	0	0	0	
+C	0	0	25	0	0	0	0	0	0	0	
+G	0	0	0	0	61	0	0	0	0	0	
+T	0	0	3	0	0	0	89	0	0	0	
+N	0	0	0	0	0	0	0	0	0	0	
diff -r 1c2db0054039 -r 161f4383df15 test-data/slamdunk_summary.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/slamdunk_summary.txt	Sun Jan 20 05:20:30 2019 -0500
@@ -0,0 +1,4 @@
+# slamdunk summary v0.3.3
+FileName	SampleName	SampleType	SampleTime	Sequenced	Mapped	Deduplicated	MQ-Filtered	Identity-Filtered	NM-Filtered	Multimap-Filtered	Retained	Counted	Annotation
+./filter/reads1.bam	sample_1	NA	-1	12	12	0	0	0	0	0	12	16	
+./filter/reads2.bam	sample_2	NA	-1	6	6	0	0	0	0	0	6	12