diff hicup2juicer.xml @ 0:396bdc215399 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicup2juicer.xml	Mon Oct 24 15:58:52 2022 +0000
@@ -0,0 +1,83 @@
+<tool id="hicup2juicer" name="Hicup to juicer converter" version="@VERSION@+galaxy0">
+    <description></description>
+    <macros>
+        <import>hicup_macros.xml</import>
+    </macros>
+    <expand macro="requirements_hicup" />
+    <command detect_errors="exit_code"><![CDATA[
+        #if $input_file.ext != 'sam':
+            #set ext='bam'
+        #else:
+            #set ext='sam'
+        #end if
+        ln -s '$input_file' input.$ext &&
+        hicup2juicer input.$ext
+    ]]>
+    </command>
+    <inputs>
+        <param name="input_file" type="data" format="qname_sorted.bam,sam" label="Output of HiCUP to convert" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Pairs in juicebox format" from_work_dir="*.prejuicer" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_file" value="dataset1_2.hicup.bam"/>
+            <output name="output" value="dataset1_2.hicup.bam.prejuicer"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+HiCUP homepage: www.bioinformatics.babraham.ac.uk/projects/hicup
+
+The hicup2juicer script converts HiCUP BAM/SAM files to a format compatible 
+with Juicer and JuiceBox( https://github.com/aidenlab/juicer ).
+Outputfiles generated by this script may be converted to Juicer ".hic" files 
+using the "pre" command as described at: https://github.com/aidenlab/juicer/wiki/Pre
+
+The script does not use restriction site coordinates when generating output.
+
+FUNCTION
+
+HiCUP generates SAM/BAM files of mapped, filtered paired-end reads 
+constituting the sequenced valid Hi-C di-tags. These may then be analysed by a 
+variety of specialised tools, but before this is possible the datasets will 
+need parsing into an appropriate format.
+
+The hicup2juicer script converts HiCUP BAM/SAM files to a tab-delimited format 
+comprising 7 columns, with read pairs on the same line:
+
+<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>
+str = strand (0 for forward, anything else for reverse)
+chr = chromosome (must be a chromosome in the genome)
+pos = position
+frag = restriction site fragment
+mapq = mapping quality score
+
+Column1: Readpair index number (starting at 1)
+Column2: forward read strand (0 = positive strand, 1 = negative strand)
+Column3: forward read chromosome name
+Column4: forward read position
+Column5: forward read fragment id (set to the dummy value 0)
+Column6: reverse read strand (0 = positive strand, 1 = negative strand)
+Column7: reverse read chromosome name
+Column8: reverse read position
+Column9: reverse read fragment id (set to the dummy value 1)
+Column10: forward read MAPQ score
+Column11: reverse read MAPQ score
+
+
+COMMAND LINE OPTIONS
+
+--help         Print help message and exit
+--version      Print the program version and exit
+--zip          Write output to a gzip file
+
+Full instructions on running the pipeline can be found at:
+www.bioinformatics.babraham.ac.uk/projects/hicup
+
+Steven Wingett, Babraham Institute, Cambridge, UK
+]]>
+    </help>
+    <expand macro="citation_hicup" />
+</tool>
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