diff hicup_mapper.xml @ 0:9ba09ebeb5aa draft

planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicup_mapper.xml	Thu Mar 09 09:32:26 2017 -0500
@@ -0,0 +1,65 @@
+<tool id="hicup_mapper" name="Hicup Mapper" version="0.1.0">
+    <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="stdio" />
+
+    <command><![CDATA[
+        BOWTIE_PATH_BASH="\$(which bowtie2)" &&
+        #set index_path = ''
+        #if str($reference_genome.source) == "history":
+           bowtie2-build "$reference_genome.own_file" genome &&
+           ln -s "$reference_genome.own_file" genome.fa &&
+           #set index_path = 'genome'
+        #else:
+           #set index_path = $reference_genome.index.fields.path
+        #end if
+        hicup_mapper
+        --index '$index_path' 
+        --bowtie2 \$BOWTIE_PATH_BASH
+
+        $input_first_sequence $input_second_sequence
+
+        ## output handling
+        && mv hicup_mapper_summary* hicup_mapper_summary.txt
+        && mv *.pair.sam result.pair.sam
+        && trunc_result_1=\$(echo '$input_first_sequence' | rev | cut -d'/' -f1 | rev)
+        && trunc_result_2=\$(echo '$input_second_sequence' | rev | cut -d'/' -f1 | rev)
+        && mv \$trunc_result_1*.mapper_barchart.svg dataset1.mapper_barchart.svg
+        && mv \$trunc_result_2*.mapper_barchart.svg dataset2.mapper_barchart.svg
+        && echo \$trunc_result_1.mapper_barchart.svg
+        && echo \$trunc_result_2.mapper_barchart.svg
+    ]]></command>
+    <inputs>
+        <expand macro="input_files" />
+        <expand macro="reference_genome_macro" />
+    </inputs>
+    <outputs>
+        <expand macro="mapper_output" />
+    </outputs>
+     <tests>
+        <test>
+            <param name="input_first_sequence" value="dataset1.trunc.fastq" ftype="fastq"/>
+            <param name="input_second_sequence" value="dataset2.trunc.fastq" ftype="fastq"/>
+            
+            <conditional name="reference_genome">
+                <param name="source" value="history" />
+                <param name="own_file" value="chr1.fa"/>
+            </conditional>
+            <output name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/>
+            <output name="result_pair" file="result.pair.sam" lines_diff="8"/>
+            <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"/>
+  
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
+
+    To get more information about the mapper visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Mapper
+    ]]></help>
+    <expand macro="citation_hicup" />
+</tool>
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