diff hicup_mapper.xml @ 5:396e8c4ebfee draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef

--- a/hicup_mapper.xml	Fri May 25 17:48:10 2018 -0400
+++ b/hicup_mapper.xml	Sat Oct 22 08:43:54 2022 +0000
@@ -1,9 +1,9 @@
-<tool id="hicup_mapper" name="Hicup Mapper" version="@VERSION@.0">
+<tool id="hicup_mapper" name="Hicup Mapper" version="@VERSION@+galaxy0">
     <description>aligns paired reads independently to a reference genome and retains reads where both partners align.</description>
     <macros>
         <import>hicup_macros.xml</import>
     </macros>
-    <expand macro="requirements_hicup" />
+    <expand macro="requirements_hicup"/>
     <command detect_errors="exit_code"><![CDATA[
         BOWTIE_PATH_BASH="\$(which bowtie2)" &&
         #set index_path = ''
@@ -15,62 +15,84 @@
            #set index_path = $reference_genome.index.fields.path
         #end if
 
-        ##Dealing with fastq and fastq.gz
-        #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
-           ln -s $input_first_sequence dataset1.gz &&
-           #set input1='dataset1.gz'
-        #else
-           ln -s $input_first_sequence dataset1 &&
-           #set input1='dataset1'
-        #end if
-
-        #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
-           ln -s $input_second_sequence dataset2.gz &&
-           #set input2='dataset2.gz'
-        #else
-           ln -s $input_second_sequence dataset2 &&
-           #set input2='dataset2'
-        #end if
-
+        ##Dealing with inputs
+        @PAIRED-END_INPUT@
 
         hicup_mapper
             --zip
             --threads \${GALAXY_SLOTS:-1}
             --index '$index_path'
             --bowtie2 \$BOWTIE_PATH_BASH
-            $input1
-            $input2
+            '$read1'
+            '$read2'
 
     ]]></command>
     <inputs>
-        <expand macro="input_files" />
-        <expand macro="reference_genome_macro" />
+        <expand macro="input_paired"/>
+        <expand macro="reference_genome_macro"/>
     </inputs>
     <outputs>
-        <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary*" label="hicup_mapper_summary.txt"/>
+        <data name="hicup_mapper_summary" format="tabular" from_work_dir="hicup_mapper_summary*" label="hicup_mapper_summary.txt"/>
         <data name="result_pair" format="qname_sorted.bam" from_work_dir="*pair.bam" label="pair.bam"/>
-        <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1*.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" />
-        <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2*.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" />
+        <collection type="list" name="mapper_barchart" label="Mapper Barchart.svg">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mapper_barchart\.svg$" directory="./" ext="svg"/>
+        </collection>
     </outputs>
-     <tests>
+    <tests>
         <test>
-            <param name="input_first_sequence" value="dataset1.trunc.fastq.gz" ftype="fastq.gz"/>
-            <param name="input_second_sequence" value="dataset2.trunc.fastq.gz" ftype="fastq.gz"/>
+            <conditional name="library">
+                <param name="type" value="paired"/>
+                <param name="input_1" value="dataset1.trunc.fastq.gz" ftype="fastq.gz"/>
+                <param name="input_2" value="dataset2.trunc.fastq.gz" ftype="fastq.gz"/>
+            </conditional>
             <conditional name="reference_genome">
-                <param name="source" value="history" />
+                <param name="source" value="history"/>
                 <param name="own_file" value="chr21And22FromHg38.fasta"/>
             </conditional>
-            <output name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/>
-            <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="8" ftype="qname_sorted.bam" />
-            <output name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/>
-            <output name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/>
+            <output name="hicup_mapper_summary">
+                <assert_contents>
+                    <has_text_matching expression="\s+99742\s+2658\s+2.7\s+3885\s+3.9\s+12437\s+12.5\s+80762\s+81.0\s+1143\s+1.1"/>
+                    <has_text_matching expression="\s+99742\s+2476\s+2.5\s+3725\s+3.7\s+12679\s+12.7\s+80862\s+81.1\s+1143\s+1.1"/>
+                </assert_contents>
+            </output>
+            <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="4" ftype="qname_sorted.bam"/>
+            <output_collection name="mapper_barchart" count="2">
+                <element name="dataset1.fq.gz" file="dataset1.mapper_barchart.svg" ftype="svg" compare="sim_size"/>
+                <element name="dataset2.fq.gz" file="dataset2.mapper_barchart.svg" ftype="svg" compare="sim_size"/>
+            </output_collection>
+        </test>
+        <test>
+            <conditional name="library">
+                <param name="type" value="paired_collection"/>
+                <param name="input_1">
+                    <collection type="paired">
+                        <element name="forward" ftype="fastq.gz" value="dataset1.trunc.fastq.gz"/>
+                        <element name="reverse" ftype="fastq.gz" value="dataset2.trunc.fastq.gz"/>
+                    </collection>
+                </param>
+            </conditional>
+            <conditional name="reference_genome">
+                <param name="source" value="history"/>
+                <param name="own_file" value="chr21And22FromHg38.fasta"/>
+            </conditional>
+            <output name="hicup_mapper_summary">
+                <assert_contents>
+                    <has_text_matching expression="\s+99742\s+2658\s+2.7\s+3885\s+3.9\s+12437\s+12.5\s+80762\s+81.0\s+1143\s+1.1"/>
+                    <has_text_matching expression="\s+99742\s+2476\s+2.5\s+3725\s+3.7\s+12679\s+12.7\s+80862\s+81.1\s+1143\s+1.1"/>
+                </assert_contents>
+            </output>
+            <output name="result_pair" file="dataset1_2.pair.bam" lines_diff="4" ftype="qname_sorted.bam"/>
+            <output_collection name="mapper_barchart" count="2">
+                <element name="dataset1.fq.gz" file="dataset1.mapper_barchart.svg" ftype="svg" compare="sim_size"/>
+                <element name="dataset2.fq.gz" file="dataset2.mapper_barchart.svg" ftype="svg" compare="sim_size"/>
+            </output_collection>
         </test>
     </tests>
     <help><![CDATA[
 
-    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
+    For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html
 
-    To get more information about the mapper visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Mapper
+    To get more information about the mapper visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-mapper
     ]]></help>
-    <expand macro="citation_hicup" />
+    <expand macro="citation_hicup"/>
 </tool>